Just finished the game, what a ride! Definitely one of the best games I have played this generation.
Having said that, and like many others have already pointed out, I think the game is far from perfect. The game feels a bit too linear and the structure of the game seems to always be clearly divided between action set pieces and exploring/supply gathering. This in the end makes the game a bit predictable which reduces the tension unnecessarily.
Then, I think gameplay wise there are three somewhat big problems, the cover system, the puzzles and the enemy/side characters AI. Those have already been covered enough and are pretty obvious so I won't get into them.
And, storywise, I think it's a shame that they did not give NPCs something more to say. In a game with such a well crafted game world it really puts me off when I see all these NPCs just standing everywhere with which I cannot interact, it really ruins the inmersion. I know it's just an action game but sometimes it really seemed like I was getting to know the story more from the notes I was finding than from what the characters were telling me.
With all that said, this game is amazing, so much fun, and the setting, characters, graphics (for the most part), ART (I love the unlockable concept art, amazing) and sound are really something else.
And like somebody said, I really wish there is a prequel to this game, not a sequel.