Hi,
I have been twice to JP with my wife... 1st trip to Matsumoto, Takayama, Shirakawa-go (
http://www.japan-guide.com/e/e5951.html) and for 2nd trip, I visited Kyoto, Tokyo, Mt Fuji and Izu area.. Both of the trips I went are on F&E and I must say the experience is terrific and we can experience the real japanese culture. (Hot spring, Ryokan)
Usually, Tour agent will usually bring u to those usual place and shopping area, but if you really want to experience Japanese culture, travelling on your own is the way to go. The transport is really convenience and you can venture to those remote area easily. As for language, if u can read chinese, that is half battle won.
You can get cheap accomodation via internet too:
These are 2 sites I booked for my trip:
http://www2.tocoo.jp/english/ (very cheap accomodation)
http://www.japaneseguesthouses.com
Please drop me a note and I can share with u my photos.