We went December 2023. I’ve been previously a couple times and this time was the worst I’ve experienced in terms of increasing tourists. (Yes, I’m aware I’m one of those too.)
For something different, we did a train (there’s a limited express from Kyoto - Gifu - Takayama - Toyama), leaving Kyoto in the morning and a day stop in Gifu to visit Gifu castle. Not so many westerners there and the staff were probably a little more surprised to see us arrive, but still setup to use voice translators to help us, but less English on signs. We then got the train through to Takayama and used that as base for day trip to Shiragawa-ko. We contacted a local guide (through the local guide’s site) and had a personal tour of the village.
Mercure Takayama was nice, and had private & communal onsen on the roof, including outdoor ones. Had the place to myself a couple times.
Wasn’t much snow around Takayama on Christmas Day but more on the ground in Shiragawa.
We then got the train through to Toyama and visited the glass museum (amazing sculptures…) though the earthquake was a few days later and we wondered how much of it survived. That was a day trip to connect Shinkansen back around to Nagano. I had to take my wife to the snow monkeys there, but it was terrible compared to previous visit. So many more people and the monkeys were almost being rounded up for the tourists this time. Very unpleasant.
You could head up that way and then back around to Kyoto via Kanazawa.
I had previously used Airbnb no problem but when looking this time, many of the check in requirements , even for private homes were wanting scans/ copies of passports and the like (sounded like for local govt requirements) and just didn’t feel comfortable handing that over to an Airbnb host. So stuck with hotels this trip.
Mercure near Kyoto station was very comfortable too.
I know others have rented cars in Japan without issue, but go read @drron’s (mis-)adventure with driving in Japan and his prison experience and it would put the Willies up you for wanting to drive there. It certainly put me off ever considering it. Trains and buses are everywhere I’ve needed to go.
Haven’t ever done the 5 lakes area around Mt Fuji but have done the Hakone loop twice from Odawara. There’s a tourist pass which gets you the scenic train, funicular railway, gondola, pirate ship & buses around the area. Can be done as a day trip from Tokyo. I believe Hakone is a popular area for Tokyo local’s to get away from the city.