We went in summer 2019.
We got the same kind of comments re Disney but it was actually one of the reasons we went initially! DD has always wanted to visit all six Disney parks so Japan was on our list. Theme parks used up 3 days of our holiday; the remaining time was spent exploring - so a good balance for us and worked well for both me, DH and DD.
This was our itinery:
Days 1-2: Flight to Tokyo, via Dubai
Day 2: Arrive in Tokyo; straight to hotel near Disney at Tokyo Bay area
Day 3: Explore Tokyo, west side
Day 4: Disneyland Tokyo
Day 5: Disney Seas
Day 6: Explore Tokyo, east side
Day 7: Explore Tokyo - Odaiba
Day 8: Bullet Train to Kyoto
Day 9: Explore Kyoto
Day 10: Explore Nara, via train
Day 11: Explore Kyoto
Day 12: Train to Osaka Bay
Day 13: Universal Studios Tokyo
Day 14: Explore Osaka
Day 15: Osaka; Osaka Bay; very late flight home via Dubai
Day 16: Arrive in UK, home
We didn't stay in a Disney hotel but we did chose to stay in a hotel near the Disney area. It is easy to get into Tokyo from there and well served by the train system. We knew we would need to be in the Disney parks early (they are very busy!) so it made sense to us to base our hotel there. We also got bigger rooms in the hotels in that area.
We stayed at Hilton Tokyo Bay and had a room which overlooked Disneyland - we could see the castle from our bedroom. Our hotel room for 3 B&B, for 6 nights, was just over £2000.
We used the Lonely Planet book for some walking/exploring itineraries for when in Tokyo, Kyoto and Osaka. It meant we say the key sights. We saw and did a lot! It was definitely not a relaxing break, but it was amazing. It's worth getting a decent guide book and doing your research beforehand. We literally had each day planned out, with walking routes and lists of places we wanted to visit. We were a little flexible about it but kept to the key plans as it meant we didn't end up wasting our time over there.
We discovered that the type of Japanese we like is the type you can get in the UK, rather than their more traditional options. There is a lot of raw egg it seems. Things like sushi, sashimi, wagyu, tempura, tapanyaki, etc can be incredible expensive in some restaurants and not all have the prices visible outside or even on the menu! Ramen and noodle dishes are relatively cheap however. It can be tricky to eat on a budget unless you do a little bit of research first - DD found some on TikTok for us!
We also budgeted in using my phone over there each day. I paid a daily rate to use my own data package. Some people prefer to get an additional SIM on arrival instead. We found it useful for the map app and also Google Translate in restaurants and in train/shuttle stations.
It wasn't a cheap holiday however! We probably spent around 15k in total inc flights, hotel, trains/shuttles, theme park tickets, food, etc.
It was fabulous and I'm so glad we went that year - had originally been planning for 2020 but changed our mind and brought it forward a year. Luckily!