I can second those locations.. thought a first AM trip to them would have been fine, but it quickly filled up.
I might also add Nijo castle to that list as well.
Other surrounding areas/sites like Momoyama or the Yasaka Shrine have their share of tourists but it's not a mob like Fushimi or Kiyomizudera can be.

As for hotels, I tend to take accessibility over a specific location so if I was to visit again, I'd probably take the Granvia at Kyoto station for easy access to JR, Kintetsu, city buses, and subway