Spec Ops the line. Granted I don't play a lot of shooters, both 1st or 3rd person but from what I played, Specs ops the line is special. It plays with you, making you question who is the good guy and the bad guy and the cost of being a "hero." It doesn't glorify or fantasize mindless violence, although you are forced to part take in it. It had great storytelling, engaging characters, beautiful presentation (even if the graphics were lacking a bit) and a fantastic ending.
The game play was responsive, unlike what most people say about it and the simple squad mechanics work wonderfully. It makes for a bit more tactical approach to fighting your way through the game. I cannot recommend it enough, even if just for the single player which is the main drive of the game anyways. I think of it as the "uncharted" of shooters, although it is not as epic as uncharted. Nevertheless, my time with the game was a blast and it was quite the challenge on the 2nd highest difficult on my first run through the game.
EDIT: If uncharted counts as a shooter, seeing as it is more action-adventure than it is third person shooter, then my vote goes to Uncharted 2, closely followed by Spec Ops and then Uncharted 3.
"Trick shot? The trick is NOT to get shot." - Lucian
