Young couple in Japan for 2 weeks

Hi, we are a young couple travelling in Japan for 2 weeks. We are arriving to Tokyo in the beginning of June and leaving from Osaka 2 weeks later. We are looking for recommendations where to stop by in between. Ideally we would visit Tokyo, Kyoto and Osaka, but we would like to stop by at smaller more remote places as well. We would like to explore some hidden and interesting parts of Japan, not just the big cities and we are not afraid of renting a car etc... Please feel free to recommend placed or itinerary. Thanks, Akos

Have you looked at the many destinations presented on this website? Especially in the Chubu region: http://www.japan-guide.com/list/e1104.html

Thank you I will have a look. I am still open to recommendations if anyone has some places that we shouldn't miss.

Make a initial itinerary and post it here, its easier to suggest places and give an better idea of what you like to do/see.
:)