Originally Posted by
travelinmanS
Western hotels are overpriced in Japan IMHO. Japanese chains seems to be consistently cheaper and their quality is fine. Anywhere else in Asia I try to stay in Marriott hotels but in Japan I just book Japanese hotels through hotels.com in the area I want to stay.
Some of the Japanese hotel rooms are a bit on the small side though so OP would have to decide if that's acceptable or not.
OP, the Ritz Carlton Kyoto is consistently mentioned as a wonderful experience. If you've got the points and you want to treat yourself, go for it. Nothing wrong with a little luxury at times. I stayed at the Hyatt Regency last year and thought it was a beautiful property though perhaps a bit of walk from some of the things you will want to visit.
For Tokyo, I'd highly recommend the Hilton Shinjuku. Shinjuku is my preferred area of Tokyo to base. Convenient access to the Tocho-mae subway line, literally just a 3 or 4 minute walk from the Hilton. Hyatt is also just across the street and at 12k points a night, is an absolute steal.