Tokyocooney's Japan forum

Hi,
We are looking forward to a trip to Japan. I lived in Japan for a couple years so long ago I can barely remember anything and my wife has never visited Japan. We would like to go for approximately four weeks visiting rural parts as well as interesting cities. I would think we should start our trip by 5 days in Tokyo then what? Can you throw some towns/cities that we should not miss. We also would like to stay in Japanese style hotels where possible. Please help me out with your suggestions and any hotel recommendations.

Thanks so much