Yea the first game isn't perfect, but it does a lot of the stuff very well. As Xessive mentioned, the shooting, but other adventury stuff I hate, it does superbly well. I have to be honest, when I didn't have a PS3, I used to wonder if the first Uncharted was praised more out of fanboyism, but it is a unique game that does innovate in a few ways.
I hadn't even heard of Naughty Dog. Was Uncharted their first game? I should get back to it, like I should a dozen other games.