Forget about the RC, HYATT or Marriott far outside Kyoto and do yourself a favor and stay in Kyoto city. You will not regret it and staying in Osaka or Nagoya means a lot of commuting and you do not have the possibility to go to your room for a break/rest.

Except for the HYATT there are no US chain properties in Kyoto, but that does not mean that Kyoto lacks good hotels. There are many nice properties in Kyoto and most of them are fairly priced. Japanese hotel standards are very different from US standards (much higher) and most people will find that Japanese 2* or 3* hotels are more than adequate and good value. We stayed at the new Shijo Kawaramachi Superhotel in Oct last year, which was very good (reasonable bf included) and great location. I would stay at this property rather than any 4* US hotel any day. It is extremely popular so you need to book well in advance.