Can only give recommendations on Tokyo since I usually only have a few days to stay in Japan on every trip.
-Skip the Tokyo Skytree if you want a viewpoint of the city. The Roppongi Hills viewpoint is 100x better and also has an interesting art museum to check out. Surrounding area of Roppongi is also one of the main areas for clubs if you're into that
-Don't fall for the ads for the Gundam cafe. It looks cool on paper but is basically Chuck E Cheese in real life
- Go Go Curry house>>>> most of the locations are really tiny compared to the more international spots, but the chicken and curry here are much better
-check out the teamLab Borderless Tokyo digital art museums. The exhibits and light shows there are amazing
-There's a multi story souvenir/electronics/snacks shop called Don Quixote. I think there's multiple locations, I just usually take people to the one in Shibuya area. My friends usually spend an hour or two in there just buying and browsing all the unique (and hilarious) items
-Speaking of Shibuya, it's the main center for shopping, nightlife, restaurants, etc along with Shinjuku
-Asakusa: traditional Japanese architecture, temples, restaurants, etc. Some of my favorite green tea ice cream and street food spots are here
-Akihabara: I'm not really into video games or anime, but it's worth checking out just for the sheer scale of all the arcades and shops they have there. Go to a maid cafe if you want to experience the weirdest cafe you'll ever go to (it's not sexual...just strange
)
-Ginza: high end shopping area. Not really much to see here but it's a more relaxed area to stay in, and it also has a restaurant called Ginza Steak House that you should check out ($$$ but really good)
There's other districts I've been to in Tokyo, but these are just the most repeat worthy IMO. It's such a massive city that you can spend days there and still not see even 50% of it