I think it's a sensible choice for Game of the Decade because so many people love it and because it was apparently so fantastic and revolutionary and innovative back in 2004. I really don't think it stands up at all against even the most average of modern FPS, but that's a different matter entirely.
Part of me would have loved for Shadow of the Colossus to get it, but that hasn't really been a very influential game.
BioShock on the other hand, would probably be my first choice. It may be based on System Shock 2, but I have never seen such excellent storytelling, atmosphere and gameplay all tied together. The characters are amazing, I love using the abilities, and the twist is fantastic and actually thought-provoking. It is one of the only FPS I have ever enjoyed, and it's in my all-time top ten. Many games have tried to emulate it, not least BioShock 2, and pretty much all of them have fallen flat.
(Former) Lead Moderator and (Eternal) VGC Detective 
