Okay, this is intriguing. Gamespot have done a large interview with Ken Levine of The-artists-previously-known-as-Irrational about Bioshock. In it, he's getting grilled about a number of issues to do with the whole what the game means thing. One of them gets an interesting response - regarding the fact the game, after all this complexity, the endings are a harsh Manichean dichotomy (i.e. You're either Jesus or Mr UltraBastard of Shitsville). He admits that it was never his intention, and the request came from "somebody up the food chain from me". Later, he elaborates...
"One of the reasons I was opposed to multiple endings is I never want to do things that have multiple digital outcomes, versus analog outcomes. I want to do it like the weapons system in the combat in BioShock. There are a million different things you can do in every combat; you can play it a million different ways. Looking into the future for the franchise, that's something I want to [figure out], that by the time you get to the ending of that choice path, you have a sense of your impact on the world through lots of little permutations rather than like a giant ending piece, if you follow my meaning.
And I think we did a reasonably good job with [the endings], but there are just two of them. And this is not a game about A and B. This is a game about one through 1 million, and all those permutations of choice. And as I think about the future of the franchise, that's where I want to take that."
There's lots more in the interview, including some impressions of the way his thoughts are going for the inevitable sequels. Especially worthwhile is his final statement where he notes "If the sales success of BioShock means anything, it means that we can trust our audience a little more". And Amen to that.