This is interesting:
In reading about the game, there's an article one of the developers participated in talking about choice in Bioshock Infinite vs. choice in Bioshock. The developer made the comment that choice didnt' work well in the original because the player was rewarded for their actions. Therefore, the player made choices based not on morality, but rather based on what decision gave them the loot they wanted, when they wanted it. They said that, for Infinite, they would make a choice system that was better focused on making the player make moral decisions based on nothing but their personal beliefs.
The article came out before the game released, so he didn't say anything further. In thinking, though, I felt like I didn't notice any real great use of choice in Bioshock Infinite. You make the choice of whether or not to abuse the inter-racial couple at the beginning of the game but both choices yield the same result. You make a choice as to wether or not to shoot the mad solider-guy, but that seemed pretty tame as well.
But then I started thinking about the scene where comstock's soldiers all stop to pray. It's completely up to the player to choose what to do to them, and it's entirely un-registered by the game. Similarly, the "honor system" store at the beginning of the game features no penalty that I know of for stealing.
How do you think moral choices should be handled in games? Must they always be acknowleged? Should they not be? Do you think bioshock did well by having a mix?