Here are a few of the things we did.
Tokyo- A Happy Pancake (recommended highly. We went to the one in Shinjuku at 945am - for a 10am opening and were first in queue
Ichiran Ramen. Best ramen ive had- and the experience/process is fun. We went around 515 and had to wait 15 minutes
Pokemon Centre (big one in Ikikeburo). Kids are into this - we also went to ones in Kyoto and Osaka.
They both played Pokemon Go whilst walking around. They hadnt played for 2 years but got into again in Japan and there are so many locals playing. Kept them entertained as there is a LOT of walking in Japan.
Free walking tour of Meiji Jingu and Harajuku. Entertaining and good to get some history and info. Harajuku is fun but CROWDED. At 9am was empty. By midday was wall to wall. Lots of interesting dessert stores there
Conveyor Sushi- kids loved ordering and seeing the dishes come flying on the belt to us
Lots of walking and checking out gacha machines, crazy stores, 7/11s!, VR places
Robot Restaurant as mentioned above
Department store food- fun seeing $250 watermelons!
TeamLab- must do!
Kyoto
Did a cool E Bike Tour we found on Air B n B. Made a break from walking
Nishiki market- great food and samples
Fushini Inari- we did a hidden hike tour on Air b n b. Recommend to get away from the crowds
Philosphers Path was beautiful
Fire RAMEN- google this. So much fun
Went to a baseball game in Osaka- atmosphere was awesome. Singing, dancing, beer! (And we dont really like baseball but worth seeing a game)
Hiroshima. Musuem was interesting and my kids got into it which surprised me. Liked learning a lot.
Miyajima. Beautiful island. Deer were fun. Good snacks and food. We did this and Hiroshima as a day trip from Kyoto.
Hakone- amazing views of Mount Fuji. Stayed in a ryokan was a different experience. Onsen. Nature.
Thats an overview. Can answer detailed questions if anyone is interested!