I recognize many of it's shortcomings (the game-y elements yanking you out of the atmosphere, the combat getting a little stale by the end, etc), but man. I haven't loved a game this much in a long time. Pretty amazing, considering how much I was anticipating it, and I basically bought a PS3 to play it.
I love the story so much that I'm playing through the game multiple times and in various sections to try and get trophies and I get worked up over scenes partially playing out, and I don't want to wreck them even though I'm just loading in to grab one conversation.
So much about the story is so clearly well thought out and just makes sense literally, symbolically, and otherwise.
I can't think of a game I've liked more emotionally in recent memory since Grim Fandango. I haven't been this attached to a game and it's characters in a long time.