Since it hasn't been mentioned here,
Fufu Kyoto opened last April to rave reviews.
If Fufu's other properties are any indication,
Fufu Kyoto is instantly a contender alongside Aman, Park Hyatt, RC and FS (and Tawaraya and Hiiragiya, among others, on the ryokan end of things.) We've stayed at Fufu's Nikko and Kawaguchiko properties, and both of them were wonderful. Nikko was absolutely phenomenal, and is now easily the top option in the area.
It manages to fuze ryokan and luxury boutique hotel sensibilities with a modern twist. It offers the intimacy of a ryokan but with the familiar (to foreigners) comfort and amenities of an actual hotel. Fufu also offers plans that don't include any meals, which is nice when you consider that Kyoto has an abundance of awesome restaurants that people should definitely try.
One huge benefit of Fufu Nikko is the fact that every single one of its 40 rooms has a real, free-flowing Onsen (natural hot springs) bath! Sure, Hoshinoya Kyoto has an Onsen, but only in their communal baths (and not in the rooms themselves.)
We're booked at Sowaka next month, but will look to try out Fufu for a (near-) future visit to Kyoto.