The original BioShock was better in going meta on the futility of choice in video games as a medium. You're going to end up doing what the game designer wants you to do. This presumes a game designer has a vision of some sort, of course, but games that don't are either bad or seen as tech demos.
Bioshock Infinite doesn't purport to give the player more than the standard illusion of choice, but I think it's more interesting how choice is handled in the narrative.
The characters think that they're making big, important decisions that reshape their world. It turns out that they weren't really.