We are not much for the bright lights, big city thing. We prefer quiet times in natural settings, good food, attractive art and architecture, and 'off the beaten path' authenticity.
Where are your main cities? Kyoto sounds like your best bet, but it would be a shame to skip Tokyo entirely. With two weeks I wouldn't plan on much more than two main towns, as you can easily do stuff around them, but there is a lot.
October is a good time, not too hot, and I think avoids any holidays, but you'll want to double check.
Kyoto: the typical spots will include walking around Kiyomizudera Temple, and the old village surrounding it.
Take a train ride from there to Fushimi Inari Shrine (thousands of tori gates), and take the hike up around the mountain for the views.
Also a short train to Nara, the temples and deer
(I have done the above twice and would again, I love Kyoto)
Toyko is basically a lot of neighborhoods. The SkyTree is nice to visit, and you're close to Asakusa from there - old Tokyo, and I would recommend the Ueno Zoo. If you like pottery and kitchen stuff, a couple hours spend up and down Kababashi Street is a lot of fun. I know you said not much for the big city, but you can't go here and not stop at Shinjuku. I'd also take a walk around Akihabara (gamer/anime paradise), especially if you're there on a weekend, just for the sites.
From there, a day trip down to Kamakura is a nice. Oh, and perhaps find a way to stop in a traditional Ryokan for a night? There are some nicer all-inclusives. We stayed in one with our own hot spring tub adjacent to our suite. Full on tatami-mat, roll out the futon at night (we checked in and I was... where's the bed?), served dinner and breakfast in our room on a low table. Anyone with back problems might find this a challenge. Not the best night's sleep I ever had...
Dinners: Plan to go to amazing sushi places that you will easily drop $200 per person. Also plan to find some Izakaya's for a fun setting for far less. You really cannot go wrong with food in Japan, unless you pick from "top ten" lists from american websites. English-menu does not mean english, it means japanese in english alphabet vs. kanji. You will want to learn a few phrases, as your hotel concierge will be the best english speaker you'll encounter there.
Oh, and you'll want to arrange in advance for a Japan rail pass, and get a metro card (not sure what they call it) when you arrive. The train system is amazing, convenient, and on time.