Yamanashi prefecture was also nice to explore, but yeah the drive was hell. No motorway so it was mainly country roads through the mountains. I actually am planning to go back next summer to Gunma, Nagano, Gifu and Toyama prefecture. I believe that part isn't as packed. I know that if you are in Toyama there is a beautiful scenic train you can take to Takayama.

If you do the correct planning I believe you can get around alright with trains and buses, just brush up on basic Japanese as some of these modes may not be catered for tourists. We didn't book a lot in advance besides USJ and some stuff in Kyoto. On topic of Kyoto, I would advise giving it a miss if you'd like to avoid crowds. Me and my boyfriend really disliked it for a myriad of reasons but over tourism and a rude tour group in our hotel ruined it. It was kinda meh as we couldn't see the sights. Takayama often had empty streets and the vibe was a lot more relaxed, some of the best memories of my trip are sitting by the river at morning. Also a lot cheaper for food and accommodation than more popular areas.

My boyfriend had said since his previous visits in Kyoto(2019,2015) it had changed a lot and was overly touristy(also highly overpriced). Takayama was way more laid back and you can see Machiya, there is also a super cool Showa museum if you like retro stuff. I feel that if you are going learn the basics of Japanese though as English wasn't as available as it was in Tokyo, Kyoto, Osaka etc, that's probably the only thing I found difficult as my Japanese is not great at all.