I know the "both sides" thing is something we're all sick of now, but there's no way Levine could have imagined what 2020+ would look like. Not to say that isn't something that's always happened, but man 2012 didn't have it to our current degree of insanity. Also I always figured the Vox were modeled more after the Russian revolution which... yeah... Stalinism was the end result, so it fits. I think that's the crux of the bad writing. You model the Vox after real world socialist uprisings, but they're predominantly black in a crazy racist planation in the sky. Now you're borrowing context from two real world things, and need to be careful about what you're saying, intentionally or not, about each of them. You have a responsibility in your messaging now. Given how it landed with you, I'd say they didn't do a great job.
Also Booker's view of it fits. He's a drunk, gambling, Pinkerton who sold his daughter. He's going to be a jaded misanthrope. Oh yeah and the part where he is also Comstock. Everything is there for us to know this is not a character we should be rooting for. But while these are facts about him, they never really make it into the "feel" of booker. So the information is there, it's just not great writing.
In contrast Elizabeth is really well done. She starts naïve and pure (if only because of the whole fucked up locked in a tower bit), and Booker does genuinely "lead the lamb astray". He's the reason she gets exposed to everything, and as a result rains fire from the sky. While we know booker is an asshole but doesn't feel like one, we definitely feel Elizabeth getting darker. I also think it's a great touch that the one that saves Elizabeth is, Elizabeth. Booker can't even take credit for that one.
I'm rambling now, I have a lot of mixed feelings on the game. It's got some really great and well done parts, and some serious blunders.