I was in Kyoto during the first week of December last year, so a little later than you but not by much. I even went to a few popular places, as I was showing a first-time Japan tourist around. But aside from the main route at Fushimi Inari, the downtown area, and the station area at peak times, I didnft find the crowds to be very bad at all. If you simply cannot resist the siren call of the most popular places in Kyoto, then you can expect them to be crowded (some of them insanely so) during the peak period of fall foliage season. The best advice for those is to go early in the day before most tour-group buses are on the prowl, and definitely give them a pass on weekends.
In terms of general advice, I think the post by JapanCustomTours is spot on. There are countless wonderful places in Kyoto that will not be crowded, especially sites that are not particularly known for fall foliage. (For example, Tofukuji is uncrowded or only moderately busy during most of the year, but completely thronged when the maples are flaming. Skip it unless you want to have lots of company.)
Among the places I visited, Kurama was not crowded at all, and neither was Arashiyama, where/when I went. I would say make a list of the gmust-seeh spots in Arashiyama (Togetsukyo, the gbamboo forest,h etc.), and then go out of your way to avoid them. Then you will probably be okay.
So even if you stay in Kyoto you can find many uncrowded places. In my experience, the places in Kyoto that are most famous (Kiyomizudera, Kinkakuji, etc.) are not the best anyway, when you inject hundreds of tourists into them. For me, their intrinsic value is offset by the unpleasantness of all those people milling around.
If you go to Nara or Uji, if you are willing to skip just the number one main attraction of each (the gdeer parkh and Byodoin) you will find all sorts of treasures, for the most part without the crowds.
One thing you do have to consider is that native Japanese tourists (i.e., people who live there) have their own lists of must-see places that tends to focus on seasonal attractions. So they will throng to places that are not necessarily on the tourist track for foreigners. However, most of them will come on the weekends, and in late November they will mob the places that are well-known for maples (Tofukuji being a good example). They will also consult recent reports to find the places where the colors are peaking. So try to find out what places are gbesth when you are there, and avoid those.
You might also be able to get good advice if you go to a tourist information center and tell them what you are looking for (i.e., uncrowded but worthwhile places to visit). Unfortunately, though, in late November the tourist information centers are probably going to be too crowded to make it worth the wait in line.
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