I'm a Japan fanboi.... and been to Japan twice. Each time i spent a whole month (4 weeks) there.
I use to live in a big city myself so whenever I went to Japan I like to move around a lot... never stay in the same city more than 3 nights.... exception is my first trip where I landed in Okinawa and spent a whole week on Miyako Jima.
As a tourist I have nothing but praise for Japan.... very friendly towards tourist in general (unless you're a jerk), very clean and safe country as well.
You will see a huge difference in the big city vs rural area as to how Japanese approach foreigners.... People are a lot more outgoing towards tourist in rural area....They tend to be a lot more shy in the cities.
A few places i would recommand :
Miyajima - Hiroshima
Miyako-jima - Okinawa
Otaru - Hokkaido
Yakushima island - Kagoshima
Kinosaki - Kansai
Shiretoko - Hokkaido
Hirosaki - Tohoku (I was there for golden week and cherry blossom) very very very crowded... but what an experience :)