With the JR Rail Pass no longer being an option for many travellers next year, the problems could get worse still.
For the past twenty/thirty years, visitors would weigh up the cost of going to/from Kyoto from Tokyo by train and decide (as it was about the same price) to get the JR Pass which encouraged a bit of tourism in places outside of the heavily trodden golden routes.
The return trip to Kyoto by shinkansen will cost (roughly) the same as before but the JR Pass is no longer on the table. Kiyomizu dera is going to be groaning with people who might have gone to Himeji or Kurashiki or Hiroshima/Miyajima, or left Kyoto earlier to fit Kanazawa into their itineraries.
There is still a LOT to see in Japan but the best experiences may need to be uncovered with a bit of research and imagination if crowds aren’t a feature of your ideal holiday.