If you’re going in 2022, I’d definitely try and get to the Inland Sea, and try to time it with one of the Setuichi triennale sessions, if it’s going ahead:
There are a collection of old island villages where artists work on installations in abandoned houses, which are opened up for a few months every three years. That whole area is worth a visit, too as you’ve got the art museums like Benesse House on Naoshima, which are open all year round.
We did that in spring 2019 as part of a two week trip. We didn’t see everything we wanted to, obviously, but I think it’s long enough to get a flavour of the country.
I’d recommend flying into and out of Tokyo, getting a Japan Rail pass, and having an itinerary something like:
- Tokyo (four nights total), including
Day trip to the Hakone ‘circuit’
Trip to the Ghibli musuem (you must book this in advance)
- Osaka (two nights total)
- Kyoto (three nights total, including a day trip to Nara, which is halfway between Kyoto and Osaka)
- Hiroshima (two nights, including a day trip to Miyajima)
- Trip to the inland sea area. Allow for two full days. You can get a ferry from Takamatsu and island hop. If you want to push the boat out, then an overnight stay at Benesse House is something really special.
- Trip to and overnight stay in Koya
That keeps everything pretty local, and minimises the long train journeys. You’ll never see it all and will want to go back as soon as you leave.
You can get companies that will arrange an itinerary, hotel bookings, train bookings etc for you, and if you’re worried about the language barrier (and Japan’s slightly backward attitude to internet booking), then they can be useful, but aren’t necessary.