Cannot be surpassed
My favourite game of all time, everything to be said has already been said about the story, the depth, replay value and impact on the player. But perhaps the best thing about MGS2 is the way it hints at the vast conspiracy within the metal gear universe, and ultimately these teasers prove to be much more satisfying than the conclusions offered in MGS4.
The boss battles are admittedly not as exciting or well designed as the first game, however the thing about these battles is that they do not in any way feel contrived. They feel like an integral part of the story, the way Raiden comes across these villains and their motivations for fighting all make sense within the narrative. The fact that you do not fight fortune is a perfect example of this, the story just did not involve Raiden fighting this enemy! This is one of many bold moves Kojima made in this game and serves as another reason it is unlike any other. This natural flow of the story and boss battles is something that was perhaps not executed as well in MGS3, i.e. you will come across each member of the cobra unit simply because they are being sent to try and kill you.
The comments Kojima makes on society and the nature of video games and the state of the world, while a little unfocused, hit harder than anything else I have experienced in any medium. I could write about this game all day, which I think indicates just how much of an achievement this game is.