I just got to the bit in the podcast where you talk about the choices not affecting the ending, which I thought was actually really clever and one of my favourite things about the game.
'Moral' choice systems have been one of this generations biggest game mechanic fads, but there's also always been a bit of a backlash against them. They've been accused of being arbitrary, being a gimmick only used for cheap replay value, and also on some occasions having a very skewed view of morality itself. One particular game that, in light of all it's other praise, got particular stick for it's moral choice system... was the original Bioshock.
The attitude to choice that this game took seemed to me like a rather meta way of Irrational Games saying that they got it wrong in regards to choice in the first Bioshock, as well as a commentary on choice in games in general. No matter how much illusion of choice a game is giving you, you're still being guided by a game world that runs on a very strict set of rules. No matter what the game is, in order to progress in the game, you have to do things the game's way. Therefore choice in games, even when it does have narrative consequences, is inherently cosmetic. As such, I actually thought it was both very clever and appropriate how they used the issue of choice as a red herring, and made pretty much the whole point of the game about how, even when you think your fate is in your hands, you are being guided by forces that you can't control and don't entirely understand, and that your choice is only possible because the opposite choice was also made an equal number of times in a different world.
EDIT: I also found that a lot of the things Susan is calling out for not being explained properly were explained perfectly adequately in my experience. For example it's stated more than once (and not just in the voxophones) that Elizabeth was kept in the tower because they needed to siphon her ability to create and control tears, otherwise she could just escape no matter where they put her. Until they were able to control her personally and use her as a figurehead, they needed to restrict her abilities so she couldn't use them against them. Comstock's racism manifests because he interprets the baptism not as a chance to repent, but as a way to justify the things he did, which was helped along by the 'White Man's Burden' attitude that was still potent in a lot of fringe Christianity at that time.