Unless you come from the tropics, you might not believe how awful Kyoto can be in the summer, mostly because it's in a basin, surrounded by mountains on three sides, with no air moving. The heat doesn't even go away much at night. Be sure to schedule frequent cold drink breaks, and don't try to do too much in one day.
If you decide to stay in Tokyo, which has the advantage of making you unpack only once, lots of places are accessible as day trips: Hakone, Nikko, Matsumoto, Sendai, even Nagano.