Gran Turismo 5, God of War 3, and Killzone 2 really don't even belong in his type of question, since they are first party games; it's like asking for Super Mario Galaxy, or Metroid Prime 3, there's no way that could happen. So it really leaves MGS4 and Final Fantasy 13.
I'd say MGS4 would be my pick, but of those two games, it's not much to choose from. MGS4 may seem cool on the surface, and if MGS2 had a good storyline, I'd be psyched about it, but MGS2 is so effed up I cannot imagine the kind of damage control to wrap up the loose ends much with what MGS4 seems to be offering, what with the female/robot/animal bosses, Metal Gears that scream like a wounded heifer, and one of the most screwed-up game characters ever, Liquid Ocelot, and such.
Final Fantasy 13, where to start? Which game? Isn't there like three of them?