Okay 1 - My High School didn't even have Philosophy. The idea of it being an available course in a middle school is just so freaking cool.
2 - C'mon, the surgeon is kinda fascinating. His increasing obsession with the idea that he's an artist is great.
3 - Bioshock IS about the Big Daddy. AND the surgeon. AND Objectivism. AND the flaws of relying on gardens for oxygen in an underwater city rather than just having a crapton of algae spread around various sections. AND the interplay of systems (or lack thereof, which is the more the case in this particular game). AND player motivations.
What I'm saying is that no piece of media is about one thing (with the possible sole exception of The Crucible). And games are most especially not about one thing. They're conversation spaces for ALL THE THINGS.