I like Bioshock a lot, but Jean-Paul LeBreton (ironically, the lead level designer of Bioshock 2) makes a good point:
The problem is that the better versed you are in game conventions, the easier it is to separate the core mechanics of a game from its fiction and theme, and thus say that a game like BioShock is a meditation on free will, the dangers of ideological extremes, and whatever else… despite the fact that you spend about 90 percent of it shooting people in the face.
The world can see this disparity more clearly, ironically by virtue of being less game-literate.