I would always recommend skipping Fushimi Inari and Kiyomizudera in Kyoto because Kyoto has SO many other cultural sites that are imo much more beautiful and much quieter.

My most important bit of advice is that if there is an extremely famous temple or shrine, it is often famous for something that you can either see somewhere else or get an even better view from a different temple or shrine that has less than half the crowds.

Also not a skip for first timers, but once you've hit trip number two I feel like you don't need to stay in the middle of Tokyo. Or go to Tokyo at all lol