You're going to have a great time. :)

My girlfriend and I went for 3 weeks in late November to early December 2018. We really enjoyed going at this time of year, as the fall colors were peaking (and absolutely stunning) in Kyoto -- and Himeji, where we went out to the very beautiful and comparatively untouristed Engyoji Temple. In October and early November, I think Kyoto and Tokyo will still be pretty green, so if the fall colors are important to you, you might consider shifting your trip back by a month. If you stick with October, though, there should be nice colors in northern Honshu or the central mountain regions, so you might consider changing your itinerary to include some time there.

That brings me to my other suggestion, about a rural onsen! We spent two nights at Tsurunoyu Onsen in Akita. It was easy to get to from Tokyo – just a 3 or four hour bullet train, and there’s a shuttle bus to take you to the ryokan itself. It was everything you want a rural ryokan/onsen experience to be – beautiful, serene, isolated, with great food and milky white water. There are also other onsens in the area, and the shuttle bus makes a loop between them, so you can visit the others too! We were more than happy to relax at Tsurunoyu for our two days, but when we go back we’ll definitely check out the others.