Probably Metal Gear Solid 2: Sons of Liberty. It basically took every single element featured in the previous game and expanded over it with such magnificent care for detail and polish, it's insane to think how did they managed to make all that. Improved third-person/first-person mechanics, the ability to lean on covers, hold-ups, passive/agressive enemy AI, radio mechanics, bodies that obstructed your movement, interactive enviroment, bazillion of easter eggs, references and comments, new and improved arsenal (even if the Nikita is a glorified puzzle weapon this time), two completely different scenarios, a hundred VR missions, and on top of all, a storyline that would serve as the franchise's pivotal structure for later sequels to come.
Over all that, there's also the meta-narrative about the postmodern deconstruction of a videogame sequel. So yeah, MGS2 is my choice here.
