Hi guys,

I want to stay two nights at an onsen town somewhere roughly between Tokyo and Kyoto (can be somewhat out of the way, but no suggestions in Hokkaido, Sendai etc, please) I'm looking for somewhere not too touristy (like Hakone), small/quaint that will likely have good scenery/koyo on November 14th and 15th and has some nice hikes. I'm going to want to just want to unwind from being in the city, do a scenic hike and spend a night or two eating some kaiseki and bathing etc,

I've looked into places like Shirahone/Takayama/Nagano prefecture and others in the J-Alps, but it seems like november is pretty gray as far as koyo/foliage....would these still be worth it in you r opinion?

Please share your suggestions for an nice onsen/onsen town or village that suits my needs. Thank you!

Did you look into Nikko ?

Autumn Leaf Spots
https://www.japan-guide.com/e/e3817.html
http://nikko-travel.jp/english/

If you are looking for an onset town in between Tokyo and Kyoto then I would recommend Arima Onsen which is in Kobe or Gero Onsen which is in Gifu. Gero onset is named as being one of Japan's three famous hot springs. And Arima onsen is also one of the three famous hot springs.

I recommend staying at Shima-Onsen, Gunma prefecture.
It's 3.5 hours away from Tokyo. But there is a non stop bus that runs Tokyo to Shima.
Shima has a lot of nature surrounding it. There is a beautiful lake, a dam and some waterfalls.
Kashiwaya Japanese style inn is good. It has three private baths. (These are free of charge!)
I hope this will help

We stayed in Shima at the Kashiwaya in May 2012 and it was a great onsen trip.
Wonderful town for hiking, relaxing and not too crowded.
Don't know the Koyo situation in November but perhaps reading some of the Trip Advisor reviews from that season you may get a clue.
I posted a trip report...
Two Day Onsen Escape from Tokyo to Shima Onsen
Photos here
http://flic.kr/s/aHsjDMKGCp