Personally, I prefer traveling to places where I have no expectations. Kyoto is a fabulous city, but after a while, I wanted to experience a place a little less known. I once went to a place called Sado Island, northeast of the main island of Japan. I didn't know anything about it before I went, just that it had a weird shape, but it was by far the best trip I've had.
It had tons of history, traditional buildings and cultural festivals dating back to the 6th or 7th centuries. The seafood was amazing, and the people were incredibly friendly. When I couldn't find a place to eat lunch, this little old grandma closed up her shop and fed me, then drove me around the island, showing me famous temples and historic spots.
You can find good food, history, and hospitality all over Japan, but Sado Island topped it for me.