We went to Tokyo, Kyoto, Osaka, Koyasan, hakone and we did day-trips to Nara and Kobe.

I really recommend staying a night or two in koyasan to visit , it's very remote but you can get there by train from Osaka and there are tons of beautiful temples to visit as well as the Okuno-in cemetary which is breathtaking. We slept in a shukubo (which is a temple which you can sleep in) and it was well worth the price for the beautiful scenery, the nice hot bath, the buddhist meditation and the traditional monk meals. There are a lot of temples who offer this service but we personally stayed in the Rengejo-in temple (but if you want to visit the cemetary during the night, which is a possiblity, I would recommend a temple closer to it since they tend to close their doors at 9 and the cemetary is quite big)

I also really enjoyed Arashiyama in Kyoto, the monkey mountain is well worth it if you like animals (it's one of the rare places in japan where they aren't exploited sadly) and there are a lot of cute cafes along the way (the main road can get a little overwhelming with tourists, but there are more breathing room than in say Gion, you can easily find less traveled streets that are charming). Not the most japanese, but I really loved Kiki's tea room there: it's a very small tea room with a charming decor, delicious scones and a huge variety of some of the best teas I've had the chance to taste.
Another Kyoto spot I enjoyed is the Maruyama park (and the Ikkyu-an cafe there) but an obscure place I really recommend is the Moan cafe on Yoshida mountain ! We happened on it by total chance and it's a little bit of a trekk there but gosh is it charming as fuck.

I really like cafes as you can see… But cafe aside, I really recommend you visit nakano broadway in Tokyo (to me it's more worth than Akihabara if you are looking for goodies, starting from the second floor there's tons of both vintage and recent second-hand goods). I also really enjoyed the Shinjuku Marui Honkan (OIOI) department store in shinjuku, just lots of good store there and when I went a few indie fashion brands. SPEAKING OF if you are interested in alt/indie fashion LaForet department store in Harajuku is a MUST GO, the lower floors have tons of small creators shop it was super interesting.

As far as Osaka goes, it was one of my favorite place we stayed at ! I just recommend walking around the different shōtengai there, depend on which one you visit there are really different kinds of shops/vibes. If you like stationery and cats I recommend checking out 'U-ARTS', it's a small shop with tons of cat-themed stationery and some writing/art supplies too, really cute. Otherwise, it's really a great city to get lost in because there are tons of cool streets with small shops and great food.

The deer park in Nara is really cute and worth the trip, the city itself is quite charming but I don't have a particular recommendation either. Kobe we went for personal reasons (my sibling was born the day of the earthquake so we went to the Kobe Earthquake Memorial Museum, which was interesting but is not a must see either if you don't have a particular interest in disasters and disaster prevention) but chinatown there was quite interesting ! Hakone is a great destination if you want a little break from the big city, there are tons of ryokans with plein-air onsen there if you can afford it and it's nice to walk along the lake, more of a chill destination though.

Hope this gives you a few ideas ! Honestly there's tons of places that looked cool and we couldn't go to so I really recommend exploring, you'll often find something cool without even searching much !