Just a quick round up of random ideas, mostly for Tokyo. Obviously these might not be your kind of thing so take with pinch of salt:
Tokyo:
Daikanyama is a nice neighbourhood to walk around.
Shimokitazawa is (or was) trendy
Harajuku, including the fashion street Takeshita Dori (Street) is I think worth a visit, especially if you’re already at Omotesando/Meiji Jingu shrine, nearby. It’s very on the tourist route.
Kagurazaka Dori (Street) is a very nice walkable street to get some food at night, with lots of lit up restaurant signs and food places crammed into a relatively narrow street and alleyways with other places to eat.
There’s an Akomeya shop at the top of this street that has Japanese food and crafts from around the country (there’s a better Akomeya in Ginza, if it’s still open, that does lunch)
Nezu Museum has a beautiful Japanese garden
Nikko is worth visiting and can be done in a day.
Kamakura also.
Uoshin Nogizaka is a fish restaurant in Nogizaka near Roppongi with a rough and ready feel. I used to go there quite a bit.
Last time we went there they had a Thai guy working there who spoke some English. I think they have a reduced English menu now but there are better things to point to around you. They do a lunch set where local workers queue for a good value meal. No choice (we had sashimi on rice the day we went). It’s a chain so there are other Uoshin’s around town that I have’t been to.
A lot of even quite expensive restaurants have good value lunch deals. No booking, just queue. I can’t remember specific places unfortunately. Daikanyama had some.
If you happen to be near this part of Aoyama, this tiny place has like 20 different kinds of matcha ice cream, different strengths, grades, regions. Madness but good. Be warned, it’s not US sized (matcha and black sesame):
Nanaya Aoyama
https://maps.app.goo.gl/RBGJEGwTkTe965r76
If you go to Yurakucho to eat at/photo the Yakitori places under the railway arches, there’s a large Biccamera shop for all your camera and other needs.
Tokyu Hands eclectic department stores might be worth a wander. There’s one in Shibuya and other places. The walk from Shibuya crossing to Shibuya Tokyu Hands takes you along Shibuya Centre Gai, the main pedestrianised shopping street in the area. There are also the swanky Seibu and Takashimaya department stores nearby. It’s an interesting area to wander and though busy, it’s not as mad as you might fear.
Last time we were in Kyoto for the red leaves, I made this google map of 15 mostly less obvious temples to avoid the crowds. We didn’t go to all of them and @Gerd will know way more than me but they’re here anyway, fwiw:
https://maps.app.goo.gl/xZGnYEwbfYn3dDDc9
He’ll also probably know more about Nara but if you need somewhere to escape the crowds there, Yoshikien Garden is a small old traditional garden that’s free to enter and quiet.
https://maps.app.goo.gl/wRM4zCrmx8VUbYMn9
(It’s round the corner from a bigger garden that looks less interesting to me and that charges quite a bit for entry)
We loved this small izakaya restaurant in Nara and have been quite a few times. It’s not open every day (details on google maps) and it’s down a small alley that can be a little hard to find. Need to look for a sign. Its logo is a yellow beanie. The young proprietor is super friendly and can help with ordering the seasonal dishes. There are seats in front of the open kitchen, which are the best for communicating with him.
Rojiura Park izakaya restaurant
https://maps.app.goo.gl/g2fXBjCAuC5bhJMQ8
