2-4 day trip - rural(ish) Japan

I'm living in Tokyo at the moment and have all of September off, so I'd like make a small 2-4 day trip and see something new. Would prefer someplace with fewer tourists, and somewhat chill. I like taking breaks at coffee/tea shops, walking around looking at shops, rather than running around all day on a tight schedule trying to get to every tourist location on the map.

I was thinking Tono in Iwate, but wasn't sure if 2+ days was too many days. I found some decently priced taxi tours around Tono and read something about renting bicycles. If 1 day is more than enough, then maybe I should add some other places that are on the way or in the vicinity.

Other ideas was Yamagata (ginzan onsen, mountain shrines and fields), Akita (not familiar with), or Shikoku (worried this might be too much for 2-3 days).

Would love some advice, tips, or suggestions.

Maybe Tono and Kamaishi?

Try YUGAWARA and MANAZURU. http://dickh.zenfolio.com/p1070795537
Yugawara is one stop before Atami on the JR Tokaido mline. The Odoriko Express trains take 1-hour 10 minutes from Tokyo.
Yugawara is an old hot springs resort and Manazuru, one stop nearer Tokyo, is a peninsula. Both scenic and should be good for bicylcling.

If you are going to visit Tono, so how about going aroud Hanamaki.

My recommendation is Miyazawa Kenji Museum, Osawa onsen.

http://www.japanguides.net/iwate/miyazawa-kenji-museum-of-hanamaki-cit...

You can use onsen bath along river with low price.

http://www.tripadvisor.jp/Attraction_Review-g1022876-d1424298-Reviews-...

Visit Gifu.
Very beautiful place.
we loved there very much.

Thanks for the suggestions! I'll look into these.