Japan (Tokyo and Kyoto) short term apartment rentals PART II. Kyushu is now off the list

For apartments in Tokyo, look at the Mimaru Suites chain. Their rooms come with full kitchens (by Japanese standards). I’ve stayed twice at the one in Ningyocho. I actually prefer the layout of the cheaper suite.

After Kyoto, perhaps the area around Hiroshima and Itsukushima would be of interest. Not really away from the tourists, but if you stay on Itsukushima I hear it quiets down after the day trippers leave.

My wife and I have dietary restrictions, so we typically look for hotels/apartments with a kitchen/kitchenette where we can make some meals.

For our most recent Kyoto trip we used booking.com with the filters for places with kitchen/kitchenette, and while the choices were limited, there were some. I also use Agoda for searching for places in Japan, though typically I book through other means.

For hiking and natural beauty:

I am currently planning a hiking trip in Shikoku. There are a lot of hiking options and Shikoku is considered much less touristed. There is also the Shimanami Kaido biking trail across the inland sea.

There is the Kumano Kodo pilgrimage trail in Wakayama. This can be done as a series of day hikes if you like. I did this in November and it was very quiet. Visiting the three major shrines, digging our own onsen into the banks of a river, enjoying the cave onsen in Hotel Urashima, eating fresh sashimi. Overall a great experience.

I have done sections of the Nakasendo Way in the Kiso Valley. Heading from Kyoto to Nagatsugawa, hiking the section from Nagiso to Magome (or the section ending in Narai), and spending a night or two in Matsumoto might be a nice slow trip back to Tokyo from Kyoto.

In my opinion Hokkaido (particularly Eastern and Central Hokkaido - Shiretoko National Park, Lake Akan, Daisetsuzan National Park) can't be beat for hiking and natural beauty in Japan. I was there in September (apparently a slower period). Quite a ways from Tokyo and Kyoto, but you may be able to swing it with domestic flights.

I have been to all four main islands and have to say Shikoku is my favorite. It is the least touristed of the main islands. It is easy to get there from Kyoto with a combination of Shinkansen then Limited Express trains from Okayama over the Seto Inland Sea. Lots of hiking options though you would need to do a bit of planning as public transport is limited though if you rent a car it opens up more possibilities. The JR Shikoku Rail Pass is a great deal if that is something that appeals. I was there last month and purchased a four day rail pass for US$95 (via Klook) which covered all the JR lines, one of the ferry lines, the private railways in the southeast and southwest and the tram lines in Matsuyama, Takamatsu and Kochi.

Since I usually arrive and depart from Tokyo, I like to take the train one way and fly the other. On my last trip I took the train from Shimane Prefecture to Takamatsu and flew back to Tokyo out of Kochi airport. On ANA I paid around US$100 for that flight in economy and ANA and JAL include a bag in their prices.
I always enjoy flying domestic flights in Japan. Board a B777 with 300 passengers in 15 minutes? Sure - no problem. Amazing. And there is usually at least one English speaking flight attendant on each flight. And they always notice me (wonder why!) and come over to check on me in English and make sure I am aware of the flight info.

Shimane Prefecture is Japan's least touristed area. In four days I only saw four other westerners the entire time I was there. Can't advise on hiking but I think there are plenty of options. Can recommend Truffles Donuts in Matsue. Where my business hotel ran under US$60 a night including breakfast. Easy to reach from Kyoto as well.

And if you are shying away from Kyushu because of the recent earthquake, I am not sure that would be a problem. We visited the Noto Peninsula last year and, while there are still plenty of signs of damage from the 2024 earthquake, people seemed happy to see us and were appreciative for visitors. Wandering around Animizu a gentleman saw us and worried we were lost offered to drive us to the train station. We weren't lost but he was so concerned we accepted. On the train up there the conductor spotted us and in his best sign language, kept pointing out sights for us. And on the return trip, he found someone on the train who spoke English and she joined us to point out sights and give us background information. All in all a great experience.

Why is Kyushu off the list?
We visited this April and loved it.
Kinisaki Onsen, with it’s many hot spring onsen is one of our hidden gems%

The earthquake was in Kumamoto. There are many wonderful places all over the island.

Thank you for these tips.

Becky, We don't know what things will look like in a month and are reluctant to travel there now and possibly get in the way. And didn't the volcano just erupt? We don't leave until the end of October, but we do need to start firming things up.

We are interested in Shikuko but ... this may sound wimpy... while we are happy to rent a small car and drive (my husband learned to drive in Tokyo although it's been many years since driving on the right). The description of driving along the winding mountain roads with limited guardrails... tbh, I am envisioning my two sons car sick in the back, vomiting, and me shrieking: OMG WATCH THE CLIFF!! (-;

Are there beautiful sites and hiking WITHOUT the narrow hairpin curves up mountains? Otherwise, I think we are now looking at for this two-week vacation, the Kii Peninsula.
So Tokyo >> Kyoto and visiting family /friends Lake Biwa >> Kii Peninsula >> Back to Tokyo and home

Although looking to see weather Kii Peninsula beginning of November

I wouldn’t hesitate to go to Kyushu because of the earthquake. The damage is in Kumamoto and there is a lot else to see on the island. I might reconsider visiting Kumamoto proper, especially if the castle stays closed. But the earthquake there is no reason to avoid the rest of the island.

I want to add something I forgot to mention in my earlier response and add an additional comment about Shikoku.

If you decide to get away from the usual tourist haunts, I would suggest making sure you have cash as a lot of small business don't take credit cards. At least that has been my experience in western Honshu and Shikoku in particular. On my recent trip I was in southwestern Shikoku when I realized my phone's battery was running very low and, while I had a battery pack, I had taken the wrong cord with me so could not charge it (or use the wall sockets at the JR station). I was thrilled to find a Daiso (Japan's amazing 100 yen store) where I had my choice of cables. But when I went to pay with my credit card the store in this particular town was cash only. Fortunately I always carry yen with me in Japan so crisis averted. And I would have had a big problem as my rail pass was on my phone and I needed it to get back to Kochi.
Heck, if you want to get cat-tail donuts in Yanaka Ginza in Tokyo, you need cash so there are still plenty of places in Japan cash comes in handy.

I won't advocate for or against driving around Shikoku but I will say Japanese infrastructure is generally excellent (and honestly better than around my home town in the States). I have ridden buses in Shikoku and never thought the roads particularly dangerous.
Here's a video with some road views: https://www.youtube.com/watch?v=gByWjbAHf28

Whatever you decide I am sure you will have a great time. I travel to Japan regularly and even though it is only a month since my last trip, I am already looking forward to my next one.