I suggest going to Tohoku area. It's the northern part of Japan, filled with nature, historical sites, and great food.
- Yamadera Temple
- Hiraizumi Temple (World Heritage)
- Shirakami Sanchi (World Heritage)
- Oirase Gorge
- Boat Cruising at Geibikei
- Mt. Hakkoda and Sukayu Onsen
- Hirosaki Castle (esp. cherry blossom)
- Matsushima Bay
Find more about Tohoku from here:
i suggest you have to visit "Shirakawa Go" in Gifu. There you will be get cool the weather and the ambience.