I thought the ending was fantastic. I kept hearing about it being great, and I was sure it was gonna have either Joel or Ellie dying. Probably Ellie, to mirror the start of the game with his daughter. I'm really glad they didn't go that route, 'cause it probably would have seemed like kind of a cop-out.
Only real complaint with the game is that they overused the "find a raft for Ellie" and "give each other a boost!" thing. They overused the boost in Uncharted 2 also. Ok, Naughty Dog, you made a neat animation, that's cool. But I did like how Ellie acknowledged this - that part where she just goes "yeah, I know...get on the fucking raft."