Probably Prince Kiocho. It's not the nicest hotel in Tokyo, but it's a solid Marriott option and often substantially lower than other options. Ritz Carlton used to be quite excellent but don't think it's been renovated for a while so may not be what you're looking for

In Kyoto, lots of great options - Ritz and Mitsui in city center, Suiran in Arashiya.

Osaka the StR is quite nice though as others have said not the best breakfast (it's fine, just unremarkable)

Hope that helps!