Most of the travel resources can be found via
- search engines
- Japan guide
- respective official website per city with suggested routes
- Japan forum on TripAdvisor, where I am a frequent contributor
Should you have any Japan travel related questions, you may comment below or on the respective pages on this website. I shall try my best to respond to your query – when I’m not on the road.
26 thoughts on “Comments”
How can one see these places if you do not drive and only use public transport? Thank you.
Where do you plan to go in Japan ? If you can be more specific it’d be easier to help.
I would like to know how much I can see or do, using a 21-day Japan Rail Pass – starting in Sapporo and making my way back to Tokyo by train. Places on my “wish list” are:
Sapporo- Otaru – Yoichi – Daisetsu-zan National Park, Shikotsu-Toya N.P – Noboribetsu Forest – Lake Toya – Hakodate – Lake Onuma – Aomori – Lake Towada – Sendai – Yamagata- Matsushima – Niigata/Sado Island – Nikki – Nagano
I would prefer to concentrate my time in Hokkaido, Tohoku and Central Honshu, and not trying to do too much in one trip. Ideally, have a few bases and do day trips from each one. Does this make sense to you?
I would also like to see Tokyo during this trip.
I think it would be unwise for me to go south of Tokyo as I think I would need another 3 weeks!
My interests are nature, shrines, scenery, walking, lakes, countryside, the snow monkeys.
Hope this helps you to understand me. I am 72 years old, who is active and enjoys the outdoors life. I really enjoy walking and I can walk for many hours in one day
Thank you for all your help. Brigid
Agree with your travel philosophy. I’d plan similarly to enjoy rather than rushing through too many spots in one trip.
To rely on public transports, use hyperdia.com to check train schedules. Consider using Takuhaibin to send luggage to next destination hotel/ryokan 1 day in advance.
Refer to a high-level travel itin by public transports below.
Hope this helps. Let me know if you have further queries.
In Hokkaido (11N)
Sapporo- Otaru – Yoichi (3N) by frequent JR commuter train based in Sapporo.
Daisetsu-zan National Park (2N) – Sapporo > Asahikawa by frequent JR Kamui express train in about 90min, then change bus to Asahidake onsen
Shikotsu-ko (1N) – Asahikawa > Sapporo > Chitose by train then change bus to Shikotsu-ko, which is a serene and beautiful lake on clear days.
Noboribetsu (1N) – Chitose > Noboribetsu by train then change bus to onsen town
Toya-ko (1or 2N if you visit Usuzan, lake cruise) – Noboribetsu > Toyako by train then change bus to onsen town. Fireworks after dinner every night from May till end Oct.
Hakodate (2N) – Toyako > Hakodate by JR Hokuto express train. Onuma NP can be visited either en route or as a day trip from Hakodate. There is a train station for Onuma NP. Don’t miss the night view on top of Mt Hakodate and better take ropeway up there to avoid traffic congestion. The seafood morning market is famous in Japan.
Amongst the old historical buildings, the ex-British Consulate has a nice tea room with tea set served overlooking a nice garden. We were there twice.
In Tohoku (about 7N)
Towada-ko (1or 2N if you visit nearby Oirase stream) – Shin-Hakodate > Shin-Aomori by Hokkaido Shinkansen then JR bus to Yasumiya in Towada-ko.
Sendai (2 or 3N) – Shin-Aomori > Sendai by Tohoku Shinkansen. Day trip to Yamadera and Matsushima Bay by JR express train in about 30min.
Niigata/Sado Island – Sendai > Omiya by Tohoku Shinkansen then change Joetsu Shinkansen to Niigata. Take ferry/jetfoils to Sado Island.
I have not visited these places and thus not in a position to make recommendations.
Niigata > Tokyo by Joetsu Shinkansen direct.
– visit the Snow monkey park as day trip or stay overnight in nearby Shibu onsen, Yudanaka onsen or in Nagano city.
Tokyo <> Nagano by Hokuriku Shinkansen, then change bus or Nagaden private train to Yudanaka onsen town.
October is the harvesting season of apples and chestnuts in farms nearby Obuse town. In Nagano city, don’t miss famous Zenkoji.
Nikko can be easily visited as day trip from Tokyo by Tohoku Shinkansen to Utsunomiya then JR Nikko train. Don’t miss World Heritage Toshogu Shrine.
For temples and shrines, consider also Kamakura about 1 hour by JR Yokosuka commuter train.
Thank you so much for all this info – it is exactly the kind of things I wish to do and see.
1. Did you stay in expensive accommodation on each trip? I am a backpacker, because I travel alone I meet other like-minded hikers in hostels or family homes – would this be a problem? Also, my budget has to include: long-haul and short- haul flights, accommodation, food, entrance fees to places of interest and a 21 day JR Pass. Do you think I would be able to get reasonable accommodation for 5000 Yen per night? Any idea what a daily budget should be – excluding JR Pass and flights.
2. During your 5 nights in Tokyo did you do the day trips as extra nights or were they INCLUDED in these 5 nights?
The more I read about Japan I am wondering if I should spend 25 days to cover the area from Haikkdo as far as Tokyo – including the day trips to Nikko, Nagano and Kamakura.
3. Do you know anything about internal flights to Sapporo from either Haneda or Narita airports?
4. I am still not sure if my best choice would be to fly directly from my international flight, on an internal flight to Sapporo as I now know that there are some flights from London which arrive in Tokyo at 1.30 pm – this would allow me enough time to take an onward flight to Haikkado.
5. I shall make a list of my must see places and prioritise them, before I write to you again.
6. I definitely feel that going south of Tokyo is not an option on my first trip. I do not want the rush from one place to another – I wish to explore at a leisurely pace – like you have done.
I hope this is not taking up too much of your time – I appreciate your help.
There might be more hostels and guesthouses in larger cities like Tokyo, Sendai and Sapporo along your itin. Note that you might have to share bathroom/toilet depending on premises. I have not stayed in this category though. You may search on the TA forum for past comments or post a new thread. Alternatively, you may check out local no-frill business hotels for budget travellers. Toyoko Inn is one of those often mentioned in the forum. It has all the basic facilities of a hotel room including own bathroom and toilet. Daily rate is around JPY10K, maybe less for single room and depending on location. However, in rural areas like Asahidake onsen, Toya-ko etc, search for pensions whose daily rates range from JPY5-10K+, including 2 meals. Most likely you’d have to share bathroom/toilet in these as well. We have stayed in pensions twice in Biei, though we picked a room with own bathroom and toilet which cost a bit more. While searching via 3rd party websites, book lodgings with free cancellation option as Japan hotels/ryokans usually allow 3 to 6 months booking in advance.
The national 21D JRP is not cheap at nearly JPY60K. After your itin is fixed, it’d be in a better position to evaluate the most valued option on rail passes. For bus trips, roughly estimate JPY1.5K for a journey over 1 hour.
Prices of normal meals have remained more or less flat over the last 20 years – due to their deflationary economy since I first visited Japan for business and subsequently personal travels. In all major cities, you could have a beef/pork/chicken rice set of less than JPY800 in 24-hour local chain shops. In the basement floor of larger department stores, cooked food in all sorts of varieties are sold at a bargain of few hundred Yen from 18:00 each day for take-away. Local vege and fruits are extremely fresh and delicious. You can smell freshly baked bread rolls from over 50m away, while patisseries are eye-catching and not sweet. In all convenience stores round every corner in major cities, you can buy bento, rice balls, sandwiches, bread rolls etc.
Thus, you may estimate a rough daily budget of JPY15-20K, excluding train rides and flights. It might be easier to meet the lower end of the budget in Hokkaido and Tohoku before you return to Tokyo.
Q2. The 5N in Tokyo that I have proposed does include day trips. If you intend to visit certain spots in Tokyo, do add days as appropriate. For 1st-timers in Tokyo, I usually recommend 4 days. Though for your interests, you may visit city parks like Shinjuku Gyoen and possibly 1 day to Takaosan for an easy hike. Don’t miss Senso-ji in Asakusa, though it’s pretty crowded most of the time. An afternoon/evening visit to Shibuya, Shinjuku and Omotesando would let you feel the vibrancy of the modern mega-metropolitan.
my visit to Takaosan in 2013.
Q3+4. Re the forum, domestic airlines like ANA and Air-DO operate cheap flights to Sapporo-Chitose in less than JPY10K one-way, much cheaper and faster than by train. From London, consult with your airlines to issue one single ticket to Sapporo-Chitose (CTS) via a transfer in Haneda (HND) or Narita (NRT). Partner airlines will arrange appropriate connections while abiding by IATA rules in allowing enough buffer for pax to transfer from international to domestic flight.
Q5. That’s fine, but if you have other questions in mind, just feel free to shoot them over.
Q6. Agree. I’d do the same to focus my visits on particular themes or spots, not just in Japan but also elsewhere in the world. After a few weeks, the law of diminishing marginal utility will start kicking in.
I have been advising other travellers on the TA forum anyway, so no worries 🙂
My husband and I plan to take a trip to Japan next year from mid May to early June for about 20 days. Our focus is the Japan Alps and Kansai, so my plan is to fly into Kansai Airport and travel in a loop before departing from the same airport. I’m trying to build an itinerary right now but have some considerations and wonder if you can give me some advice.
1) Is the weather in the Alps still too cold in mid May? Does it make a difference if I schedule the Alps in the beginning or end of the itinerary?
2) What will be the most efficient route for visiting the following places: Tateyama-Kurobe Alpine Route, Takayama, Shirakawa-go, Shin-Hotaka Onsen, Gero Onsen, Kanazawa, Kyoto, and Nara? Is it wise to add Hiroshima?
3) What regional rail passes will best suit my purposes? Can I still make use of the regional passes if I want a more relaxed pace since those five or seven day passes are all based on consecutive days?
I was amazed at your extensive travels in Japan and would really appreciate the assistance.
1. May is in general Spring in Japan (except in higher elevations such as the Alpine route). Thus weather is pleasant and good time for visiting those locations. If you’re worried about cold weather, better cross the Alpine route towards end May/early June. Besides, it’d less crowded for the Snow-wall walk which is the main theme till late June.
2. Consider a high level itin to avoid backtracking :
– 1st week in Kansai area including Kyoto and Nara (Hiroshima/Miyajima can be added but better stay 1 to 2 nights for a less rushed trip. Buy a 5-day JR West Kansai Hiroshima Pass (KHP) ONLY IF you visit the latter.
– 2nd to 3rd week Kyoto > Gero onsen (1N) via Nagoya > Takayama (1N) > Kanazawa (2N) while stopping over Shirakawa-go for few hours by Nohi bus > crossing the Alpine route via Toyama and exit in Shinano-Omachi onsen (1N) > Shin-hotaka onsen (1N) via Matsumoto > Kyoto via Nagoya
Matsumoto is a good base to visit other JP Alps locations such as Kamikochi, Kiso valley etc.
Notes – days suggested in the JP Alps are the minimum to explore without rushing. You may adjust according to your travel pace.
3. The JR regional passes in Central Japan and Kansai are by consecutive days. This 5-day Alpine-Takayama-Matsumoto Area Tourist Pass might be more relevant to your itin though the whole loop needs to be completed in 5 days to payoff.
Otherwise, just buy the JR option ticket for crossing the Alpine route one-way.
you may refer to our trip in late May 2007 covering parts of the JP Alps in 1 week.
Thank you so much. I’ll take your advice and work from there.
hi, loved reading your articles and it is really useful.
I am planning a trip to be in Tokyo Nartia airport on 22 Sep 2018. Leave on 9 Oct 2018
Could you guide me on what should i do for these 18 days?
Should i cover Kyushu, Osaka, Ishikawa, Toyama area, the head to Hokkaido on 3 Oct to catch the Autumn leaves before returning to Tokyo on 6 Oct to shop in Tokyo then leave?
That is my initial thought.
You can email me at firstname.lastname@example.org
So much thanks!!!
Is this your first visit to Japan ? What are your interests ?
With 18 days, consider the golden route where most tourists cover both the modern and historical Japan. e.g.
Tokyo > Kyoto/Nara/Osaka > Hiroshima/Miyajima > Kanazawa > Tokyo
Better visit Kyushu and Hokkaido as separate trips by car to explore the countryside where public transports are less efficient. Besides, the city areas like Sapporo would have peak koyo by late Oct.
For koyo (fall foliage) consider crossing the Alpine route where it’d be at peak in Murodo @2400m in early Oct.
My crossing in mid-Oct 2010.
refer also to Japan guide with suggested itin
Hello! Your info is very helpful. What rental car company do you use so as to avoid drop off fees in same prefecture–like in your trip from Wakayama to Koya to Kumano to the beach town? Thank you!
I always rent directly from Toyota Rentacar online. You may obtain online quotations and including from other car rentals/brokers in Japan.
We are a couple travelling with 3 kids of aged 8, 5 and 3. We will be arriving and departing from Hiroshima airport. Arriving on 2June2019 9am and leaving on 13June 2019 10:25am for a 11 full days trip in western Japan.
We hope to visit Hiroshima, Yamaguchi and Wakayama. Ideally, have just one base in each of the 3 areas and do day trips from each one. Minimising hotel transfer as we are travelling with young kids.
Does it make sense to you that we are spreading out the area of coverage? Do you think it is better to just concentrate on either Hiroshima, Kansai-Wakayama area only or Hiroshima, Yamaguchi-Hakata area only?
This will determine if I should purchase the JR Sanyo Sanin area pass or to buy the JR Kansai Hiroshima area pass.
I am working on the itinerary so that I can start booking accommodation however there are many uncertainties I have while planning.
I hope to get some advise and suggestions on my itinerary as well as transportation passes, self driving tips in Japan and and scenic route to consider.
Places on our wish list are:
> 1 day city sightseeing at the common tourist spots
> 1 day at Miyajima Island
> 1 day Okunoshima Island and Iwakuni bridge
Question 1a) any interesting nature sightseeing spots to suggest, to add or to replace from the above within Hiroshima?
Question 1b) Which “Visit Hiroshima Tourist Pass” (small,middle or wide) will cover Okunoshima Island and Iwakuni bridge?
Question 1c) is it worth visiting Okunoshima Island and Iwakuni bridge if time is a factor?
2) Yamaguchi – pickup and return car at Hiroshima
> Tsuenoshima Ohashi Bridge and the island surrounding.
> Motonosumi Inari Shrine
> Akiyoshio cave
Question 2a) we are considering to rent car for visiting these sites. Do you think it is crazy to do a day road trip from Hiroshima to cover all 3 sites?
Question 2b) if need to stay 1 night just to break up the journey, where is a good stopping base before heading back to Hiroshima?
Question 2c) may I ask for your opinion in which sequence should we cover these 3 spots?
Question 2d) any other interesting nature sites between these spots and the drive back to Hiroshima that worth seeing just to break up the journey?
Question 2e) Google map usually gives 2-3 driving routes, along coastal or inner land. May I know where to get information on the toll charges and how many tolls there will be in any particular route that we decide to drive from google map?
Day 1 – travelling from Hiroshima to Wakayama.
> riding on Wakayama electric railway and sightseeing any interesting stops along Kishigawa line.
> Visiting Marina City (Kuroshio Market).
> Wakayama castle (might visit on day 5 before heading back to Hiroshima by train)
> Ohashi Roka Bridge (same as Wakayama castle schedule)
Day 2 – Kumano and Hongu (renting car)
> Yunomine Onsen district
> Kawayu Onsen
> Nachi Falls
Day 3 – Shirahama (either a continuous driving trip from day 2 or by public transport if day 2 is just a day trip)
> Shirahama Beach
> Scannbeki Cavern
> Engetsutu Island
Day 4 – shirahama
> Adventures World
Day 5 – heading back to Hiroshima
Question 3a) Where to stay? To stay near Wakayama station, Kii Tanabe or Shirahama as base for the 5 days itinerary? Minimise hotel changing.
Question 3b) is it better to swap day 4 with day 1?
Question 3c) Google map shows 3 different routes, which will be your preferred route? Any difference in its toll charges?
Question 3d) where can get information on the toll charges for these routes?
Question 3e) which is a better sequence for day 2 and day 3?
Question 3f) is it possible to do a day road trip for day 2 without staying a night near the Onsen area?
Question 3g) is it easy to find food around the Onsen area/district?
Question 3f) you were there in late May, could you share the weather then?
Lastly, upon arriving Hiroshima Airport, which section should we cover 1st? Hiroshima, Yamaguchi or Wakayama?
We definitely have to be at Hiroshima on the 11th day and night as close to Hiroshima airport as possible because our flight back is 10:25am on the 12th day.
Hope you could share your opinion and suggestions for my itinerary.
Appreciate and thank you very much.
just returned from 3-week travel in Europe. My first response has just been emailed directly.
Yes, I have received. Thank you very much for your reply despite the jet lag.
Hello DLi hk,
We love reading your posts learning about amazing spots in Japan!
We are a couple that plan to visit Japan in coming Oct (2019).
We would like to have your advice based on your numerus visits to this lovely country.
It won’t be our first visit to Japan. We had one trip where we visited Kyoto, Tokyo and two days in Tohoku region. I also visited Tokyo several times for business.
This time, we would like to spend 5 days experiencing Koyo watching and finish with 4 days in Tokyo with at least one day trip to Nikko (Total of 9 full days for the entire trip).
We will arrive to Japan on the evening of Oct 12 and leave on the morning of Oct 22.
We like to focus on outdoor hiking activities along with Onsen experience and good food. We do not want to rush through too many places briefly. We also are trying to avoid over touristic spots.
We thought about two options for the Koyo watching part, hoping to get some advice with optimal itinerary:
1. Spend 5 days in Hokkaido doing a round trip with rental car from Chitose airport. Thought about places in the west / south area such as: Lake Shikotsu, Toya Lake, Noboribetsu, Niseko (Mt. Yotei), Hoheikyo / Jozankei, Shakotan / Shimamui Coast, Otaru and Sapporo.
a. How would you plan the accommodations? We thought about the following:
i. Oct 12 – arrive to Sapporo with train from Chitose. Spend the night in Sapporo.
ii. Oct 13 – Jozankei / Hoheiko by car / bus. Spend the night in Sapporo.
iii. Oct 14 – Sapporo half day -> rental car to Lake Shikotsu / Mt. Tarume. Spend the night in Lake Shikotsu area (Onsen).
iv. Oct 15 – Noboribetsu. Spend the night there in Onsen.
v. Oct 16 – Toya Lake, Niseko. Spend the night in Niseko area?
vi. Oct 17 –
1. Option 1: hike in Niseko area and drive back to Chitose airport to return car and catch a flight at 17:00.
2. Option 2: drive along the Shimamui coast, Otaru and back to the airport.
b. Should we think adding other locations such as: Hakodate, Daisetsuzan national park, Akan Mashu national park? Obviously, we will have to remove other locations in case we include these.
c. We understand that the Koyo should be in its best in mid Oct (when we arrive) in the areas southern to Sapporo. Is that correct?
d. Does it make sense to rent a car for the entire 5 days or would you start in Sapporo for 1 or 2 nights and rent a car for only 3 days?
2. Spend the 5 days in the JP Alps. Thought about the following places: Tateyama-Kurobe Alpine Route, Takayama, Shirakawa-go, Shin-Hotaka Onsen, Kamikochi, Gero Onsen, Kiso Valley, Kanazawa, Matsumoto, Nagano, Yudanka onsen and Yamanouchi Monkeys Park.
a. We realize that the above list has too many locations to travel in 5 days. We are looking for the best Koyo spots. What would you recommend?
b. Is it wise to rent a car, let’s say in Nagoya for the entire 5 days, or better to use the train system? Does it make sense to rent in Nagoya? There is an option to arrive in Nagoya airport. If we where should we return the car assuming we are moving to Tokyo?
c. We thought about possible plan:
i. Oct 12 – arrive to Nagoya airport. Spend the night in Nagoya.
ii. Oct 13 – Gero Onsen. Spend the night there.
iii. Oct 14 – Takayama -> Shin-Hotaka Onsen. Spend the night in Shin-Hotaka.
iv. Oct 15 – hiking in Shin-Hotaka area / Kamikochi. Spend the night in Shin-Hotaka.
v. Oct 16 – Tateyama-Kurobe Alpine Route (round-trip) -> without moving to the Tateyama side. Spend the night in Matsumoto / Nagano / Yudanka onsen?
vi. Oct 17 – visit Yamanouchi Monkeys Park. Return the car in Matsumoto / Nagano and move with train to Tokyo.
It’s already too much text… Anyway, would love to hear your comments.
Merry Christmas !
>>This time, we would like to spend 5 days experiencing Koyo watching and finish with 4 days in Tokyo with at least one day trip to Nikko (Total of 9 full days for the entire trip).
We will arrive to Japan on the evening of Oct 12 and leave on the morning of Oct 22.<< In that timeline, koyo would be most gorgeous in the JP Alps and in Okunikko with more hiking/trekking options. Better visit koyo in Hokkaido in another dedicated trip. On a high level with only 5 days, consider Tokyo > Nagano (1N) including dropping by the snow monkey park > crossing the Alpine route from east to west, overnight in Murodo @2400m (1N) > hiking/trekking in the Murodo side before exiting to Toyama (1N) > pick up car and drive to Shin-hotaka ropeway, stay overnight in Oku-hida onsen-go (1N) > visit Kamikochi @1400m as day trip and return car in Matsumoto, take JR express train back to Tokyo/Shinjuku.
Note that one-way drop-off fee will be levied on top of other car rental fees.
The itin is roughly similar to my koyo visit in Oct 2010, except that we relied on public transports, and did not divert to the snow monkey park.
While in Tokyo, visit Okunikko for peak koyo from Chuzenji-ko @1300m to Yumoto onsen @1500m. Visit on weekdays to avoid long line of cars and buses along the single-laned mountain road.
My 5th visit to Okunikko.
Ps. Usual peak koyo for Takayama and Shirakawa-go is end Oct to early Nov, whereas Kanazawa is around mid-Nov.
some texts have been truncated in my reply above.
resend the truncated as below, rest are the same…
In that timeline, koyo would be most gorgeous in the JP Alps and in Okunikko with more hiking/trekking options. Better visit koyo in Hokkaido in another dedicated trip.
On a high level with only 5 days, consider
Tokyo > Nagano (1N) including dropping by the snow monkey park > crossing the Alpine route east to west, overnight in Murodo @2400m (1N) > hiking/trekking in the Murodo side before exiting to Toyama (1N) > pick up car and drive to Shin-hotaka ropeway, stay overnight in Oku-hida onsen (1N) > visit Kamikochi @1400m as day trip and return car in Matsumoto, take JR express train back to Tokyo/Shinjuku.
Amanda in Sapporo here!! Know you from Trip Advisor – and we met over Genghiskan dinner in Sapporo Snow Festival many years ago??? Happy to find your blog and the great pics….hope to meet you again one day!
I’m still living in Sapporo – teaching/writing and now tour guiding too…
Thank you for the compliment.
No, I have not visited the Sapporo Snow Festival.
Wife and I will be in Daisetsuzan next week for koyo (3rd time), will be in Sapporo for 2 nights before departure.
Its really amazing that you have been to Japan >80 times. That is inspiring so I am thinking of making a trip there on my own (all this while I travel with travel agencies for the convenience). My first worry is that how am I going to ask for directions since the Japs do not speak English? Please give some advice and tips. TQ.
There is no need to worry re language especially visiting large cities where signs are in both Japanese and English. In general, converse in simple English very slowly.
Refer to below website for plenty of travel info, including suggested itin etc.
btw, avoid using “japs” as that is insulting – either Japanese or locals is appropriate.
Dear Dli, we have been communicating using the TA forums, this is how I came across this blog from you,
Re our self-drive trip I noticed you seems to take the train to an area, rent a car make your tour go to the next place by train and rent a car again.
I am starting to wonder if that would be an option the reason I was not considering this is luggage, we travel between 1 and 2,3 months every trip, our age we are 70+ the convenience etc and previous experiences. However I must say that Japan is different compared with any other country I know of, what makes it obviously also so attractive.
What are your thoughts on the above? given the fact that we do not have time issues and do not feel the need to be excited every minute of the day, there for we like to take it easy.
PS great blog, you are very fortunate to be able to travel so much and generous to share your experiences
Thank you for the compliments 🙂
Whenever I plan a trip in Japan, I’d maximise the usage of efficient public transports vs self-driving in planning an itin.
In general, I drive in rural areas where it’s less accessible/efficient by public transports. In cities, we commute using public transports only. As daily car rental + parking fee etc is not cheap, I tend to pick up a car when leaving a city to explore in rural areas.
In Japan, use the ubiquitous luggage delivery service by forwarding your luggage to next hotels/ryokans at least 1 day in advance.
Even in Kyushu, wife and I usually send 1 large luggage to next hotels/ryokans where we’d checkin 3 to 4 days later. By keeping 1 piece of luggage for the next 3 to 4 days, it’s easier to handle either by car or by train.
Beware that your idea of staying in rural areas only might not work so well in Japan where most proper hotels are in urban areas. In your case, check out if Route Inn, Toyoko Inn, Comfort Inn have premises in city suburbs where overnight parking fee might be waived or less expensive – no experience except probably once/twice in Hokkaido.
Although you’re not interested to stay in onsen, the half-board overnight package offered by most onsen ryokans in Kyushu are in-expensive at (< JPY15K per head for 2 ppl sharing a room), yet they offer good quality food and hospitality not found elsewhere in Japan, e.g. Ureshino onsen, Takeo onsen, Unzen onsen, Beppu etc. Hope this helps. ps. Maybe I can outline a high level itin in Kyushu tomorrow (based on your original itin) and communicate to you via PM in TA. cheers, dli
You have been in many places including Kyushu but not visited Yakushima, is this because you have to make chooses or is it because you did not think it was worth it ?