Japan itinerary

Hi,
We are travelling to Japan at the end of May and have almost nailed our itinerary, but we have a day and a half we haven't filled. I'm hoping to find some recommendations of how to fill this time. Our trip is pretty city heavy, so we were looking to find something that is more "back to nature" or rural Japan. We looked into do the walk from Magone to Tsumago, but its too complicated to get there and back. We will be leaving Kinosaki around noon, have that afternoon and the full next day, ending in Tokyo

Here's what we have so far:
Day 1: Arrive tokyo, train to Kyoto
Day 2: Kyoto
Day 3: Nara
Day 4: Kyoto
Day 5: Kinosaki onsen
Day 6: Leave Kinosaki around 11am HALF DAY HERE
Day 7: FULL DAY HERE end on Tokyo
Day 8-10 Tokyo

Thanks for your help

Whilst it might seem you have a half day after leaving Kinosaki Onsen, there's actually a fair bit of travel time ahead of you. For example, to Takayama you're looking at about 7 hours on a train. Same for Nagano (plus more if you headed to Shibu Onsen from there). Even for Ise or Koyasan it'll be about 5 hours. If you're happy with that travel time I'd suggest one of those or somewhere nearby in Wakayama or Mie Prefectures.
http://www.japan-guide.com/e/e4900.html
http://www.japan-guide.com/e/e4310.html
http://www.japan-guide.com/e/e4950.html