I need advice for a honeymoon in Japan!

My fiancé and I intend to honeymoon in Japan in April 2022. We hope to be able to stay for 3 weeks, and I am the type of gal who makes a fully detailed itinerary, even for a restful vacation. Neither one of us has ever been to Japan and we're having a hard time knowing what to see and what to do because it seems EVERYTHING is advertised as beautiful– and I would believe it all is too. I could really use some suggestions from what cities to see down to good places to eat. I'll detail some of our preferences if it helps narrow down suggestions.

We'd like to see some of the metropolis (but no tight, closed spaces because of my claustrophobia), but we would mostly like to see the historic and cultural areas of Japan. We're looking to have 3 main areas to stay at (Tokyo, Kyoto, Takayama) and take day trips to all the other destinations. We would love to see the natural beauty of Japan, but there's so many beautiful places we have a hard time narrowing it down. In terms of lodging, we would require our own bathroom facilities, double bed, and basically whatever a Westerner would probably want in their hotel, but it doesnt need to be super spacious. For some of the honeymoon we would like to stay at a traditional ryokan. However, I heard the bath water can be very hot and my fiancé has such sensitive skin that he can't even use Western hot tubs. I've heard that some ryokan will have personal patios with baths that you can adjust the temp on? I think we're trying to find a traditional ryokan that would offer that amenity so my partner can actually clean himself lol

Some places we've been recommended to see are: Tokyo, Kyoto, Hida-Takayama, Nikko, Tsumago, Nara, Kawagoe, Hakone, Shirakawago and a recommendation to see Hitsujiyama Park