Free Will revisited

Now that I've played Bioshock all the way through, I'm reminded of that post I made about the deconstruction of free will. So how does the idea hold up now I've taken the plunge into Rapture?

Well much of the success of Bioshock can be attributed to it's handling of free will. The player spends most of the game being guided through it by Atlas on the basis that he knows exactly what's going on. Thus the player follows an instinct that he is the game's entry point and the more they follow, more will be revealed about this game and the rules it hands the players. However, halfway through the game, the rug is pulled from under the player and it becomes clear they've been played for fools. Whilst not to give too much away, the eventual confrontation with Andrew Ryan involves him chastising the player character (ie YOU) for following Atlas' guidance without question. Thus the phrases 'would you kindly' and 'a man chooses' come across as having more weight than first realized.

So how does my idea stand up? Well I can see some similarities between my idea and Bioshock. But I should stress that I came up with my idea well before I sat down and played Bioshock - and even then my knowledge of the world of Rapture was based on scraps of information (ie Bioshock = System Shock gone steampunk; Andrew Ryan = We R Ayn Rand).
But I can see a difference in that my game has a named character whilst the character in Bioshock is pretty much the Player - and this makes a huge difference in building a connection, and a personable one at that, with the players themselves. Thus the choices presented to the player encourages them to seriously think and having moments taken out of the player's control, ie the afore-mentioned confrontation with Andrew Ryan, will certainly create an impact on the player.

So is there a place for my idea? Well, I can't see any where that Bioshock did better - still the idea of a guy mistakenly gunning down his liberators has at least some potential. And said guy refusing free will for a fabrication could be put to good use...