That's an excellent question. Often it's a case of finding a lesser known "little sister" of the overtouristed place.
A good start is to simply search on "alternatives to ..."
For Prague for example, this result came up:
The European town that's a ‘prettier’ Prague alternative — without the stag dos
eg: Instead of Amsterdam consider Utrecht, for every Lake Como, there is a Lake Orta, for Hamptons there's Cape Cod, for Tuscany there is an Umbria, for Japan there is Korea, And so on
Just on that last one, you mentioned:
The Japanese are definitely getting jaded and weary of foreign tourists. On our last trip, we dedicated more time to Korea. This was quite a contrast. Korea is still in the emerging phase for western tourists, only getting a fraction of what Japan sees. They are incredibly welcoming.
Great country and will go back