Because it's one of the few games out there to take a genuine, intelligent look at its underlying mechanics and it's nature as a game.
While a game like Mass Effect or Fallout 3 have a huge story that's interesting to take in, the problem is that they're blissfully ignorant of their limitations as a medium. Fallout 3 and Mass Effect both try to present moral dilemmas. However, for the most part, all the games have to say is "hey! isn't it cool to be a bad ass and save the world?" Despite all of the nominal freedom in Mass Effect and Fallout 3, the player is ultimately
unable to control how they ultimately act.
Contrast this with Bioshock. The game has all of the trapping of choice and freedom, but the player is ultimately limited. Even the game's nominal moral choice is ultimately meaningless, as the player gets roughly the same benefits. Aside from this, the game, being a shooter, essentially forces the player to kill tons and tons of people. It's doubtful that the player would even have second thoughts about gunning down several people. Now, if this is all that the game had to offer, it would have been just another game, but the fact that it actually, rather than force the appearance of freedom into everything, decided to instead make the fundamental lack of freedom into part of the story. It's genuine deconstruction and critique, something that neither Fallout 3 or Mass Effect can lay claim to have done or even attempted.