We're in the same predicament. Wanted to do Osaka, Kyoto and Tokyo but most hotels in Kyoto are sold out for our dates in Nov and the rates are astronomically high.

So we now have 5 nights in Osaka and 5 in Tokyo. Given that Universal Studios will take up a day is it really that bad daytripping to Kyoto? The StRegis is reasonable but I refuse to pay around $700 for a 28 sqm at the HR Kyoto.