The story, characters, and message are all top notch. Nothing is ham-fisted, and the realization of the player becoming Joel is so fucking cool and a genius way to provide commentary on violent video games in a non-patronizing way.
Unfortunately, certain issues I have with how Uncharted was handled seem to be a mainstay for Naughty Dog at this time. Most of the non-combat scenarios were very linear and I think the level design could have benefited from a more open plan, encouraging more exploration and different ways to take on a combat scenario.