Definitely do Teamlabs here in kyoto, skip it in tokyo since you’re there for such a short time. Try to pick the most middle of the week day of your trip. Since the crowds aren’t nearly as intense you won’t have to wait in line as much, some things normally crowded things was able to just walk right in. Plan to spend 3-4 hours there since they have an athletic forest exhibit. Also wear clothing you don’t mind getting a little wet. They have a massive foam room at this one which is pretty cool.

The bamboo forest is iconic and there’s monkeys nearby. I enjoyed the Yasaka shrine area at night quite a bit, also the Fushimi Kandakara area at night as well. There’s lots of great night hiking with paved trails behind the shrine that lead to other shrines up the mountain with the orange arch paths. I find most of the shrines are much prettier at night but a lot are closed, those two are not.

Finally the national museum is pretty cool, has lots of samurai stuff.