@ntm: I think I get what you're saying, but there are more problems with the subplots than the fact they don't take center stage. For example, in the Revolution-is-winning alternate universe, Booker has become a hero for helping the rebels. And while, sure, Daisy (that was her name, right? I hope that isn't racist) gives you a line about being more good to her as a martyr, that doesn't explain why literally every member of her organization who is supposed to revere you doesn't for a moment question their orders to attack.
The game just doesn't expend any effort whatsoever justifying itself, it just says, "here's the situation, roll with it". That's probably how Booker perceives things, but that doesn't make it interesting, and if a game that's all about its story is not interesting in some parts, then shouldn't that detract from it?