2-3 Kyoto
1-2 Tokyo.
Whenever we visit Japan we'll use the two towns as the hub for day trips.
My wife and 13yo grandson just got back from a 2 week trip. My grandson's favorite places were Miyako jima, Nikko and Akihabara (no surprise).
This info is a little dated, but hopefully it's mostly helpful.
P.S. cash is king.
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