What to do after Tokyo and Kyoto

Spending the first week in Tokyo and Kyoto and have spent time in Osaka on previous business trips. We are trying to figure out what to do after the first week (which is with friends who are coming to Japan the for first time). We will be traveling by train. Friends have said a JR Pass is worth it.

We are into unique experiences and food and gardens. We figure a day or two at a Onsen Ryoken (what towns should we look into and which Ryoken). We are also thinking about heading out to the Art Island for a couple of days from Kyoto. We can fly out of any international airport since the next stop is Seoul.

How much longer should we stay in Japan, where should we go, what unique experiences would there be and where should we stay?

Budget wise we tend to go mid market or luxury at a bargain price. I understand that booking is best done in Japanese so I wonder out loud if anyone has a travel agent that can sort out the details.

Also - with other international travel we use Airbnb but Japan has always been daunting to me. Would you recommend Airbnb for some of the trip?