I just keep coming back.
Everybody complains about Raiden. He's really not that bad, at worst he's great comic relief and you still get to see Snake and what a major badass he is. It's almost better not to be in control of Snake because if you were it wouldn't be as awe inspiring to see him do what he does in the cut-scenes. You get the feeling that you are a junior elite watching the master of all masters. I have to say that the main reason I play it through over and over again is to watch the cut-scenes of Snake.
As for replay value, beyond the story, collecting all of the dogtags on every difficutly is fun, and then flying through the game with the modes you can unlock is just as much fun. Trying to make it through without killing a single person is just as enjoyable as turning the platform into a bloody mess, just waiting and hoping that they send more reinforcements.
So what did we learn here? You can't beat the controls, the graphics are great, the story is twisty and turn-y and entertaining-y, and you can play it over and over again having just as much, or more fun than the first time. What more do you want from a game?