I think it's hard to predict the impact of changes to rail passes. One possibility is that more people take up regional passes to explore Tohoku or Kyushu... but who knows? In terms of raw numbers, however, I think Japan is going to see more and more visitors, so yeah Kyoto's problems will get worse. The total number of inbound visitors now exceeds pre-pandemic levels despite the fact that the number of visitors from mainland China is still relatively low.

As others have pointed out, Kyoto's top attractions are a mess but the second-tier spots are still quite calm. My last two visits have been wonderful. I took friends around Myoshinji in early summer. They were delighted by the gardens at Keishunin, which we had almost to ourselves; An ideal way for them to decompress from the crowds at Kinkakuji and Ryoanji. Of course, they needed to see those A-list temples, but I waited at a cafe while they were there. Similarly, in October, I spent a relaxing afternoon exploring Tofukuji with a friend, who is on an extended stay in Kyoto. We were there before the foliage was at its autumnal best ... He decided to go back in late October to see it in reds and yellows. I am sure that it must have been more crowded at peak foliage-viewing season, but still not as over-crowded as Fushimi Inari shrine just two stations down the line.