I'm coming around to it, but I wish there was a solid moment where Comstock explained his views and reasons, maybe even to the point where Booker would hesitate in killing off this other version of himself. Explain it in such a way that Booker would be momentarily seduced by the point of view, since they are the same person after all.
Unbaptized Booker chose to live with the weight of what he'd done. He started out racist, and this led to the massacre at Wounded Knee. But somewhere along the line he realized, "Holy shit, I killed
people." The unbaptized Booker is the Booker who chose to live with that realization, and all of the crushing depression that ensued, sending him down a spiral of drinking and debt. Even though he's at the bottom of the barrel, he doesn't deny what he did was wrong; if anything, living with that guilt keeps him down. The key thing is, -this- Booker has now recognized the ugly side of racism.
Baptized Booker, on the other hand, was "born again" -- what was past, was past. And then he thinks, "There's a God, and what's this, not only does baptism excuse my past actions, but the Old Testament justifies them: Sodom and Gomorrah, Noah's Ark, etc." As Comstock says in one recording, ill treatment of other races -is- cruel, but so was God when he wiped the earth clean with the Great Flood. Cruelty, Comstock says, can be instructive.
The two outcomes of Booker, then, would never see eye to eye. They choose different paths in life. The men they became stand on opposite sides. And the Booker we play sees the horror of what Comstock has become -- a worse monster than the one he now regrets being at Wounded Knee.
I was also hoping for something that explains how one man takes on thousands of soldiers and survives. I like the notion that coming back from death is a different Booker, but there were long stretches where I survived when it felt too videogame-y. I was also hoping for an explanation on the vigors. Why Booker has so many to access at once, and almost no one else uses them even when the bottles seem pretty plentiful. I miss Bioshock's ability to explain all of its technology in a way that wasn't using QUANTUM MECHANICS the same way Kojima uses NANOMACHINES.
RE: taking on thousands of soldiers: ...videogames. At least the fights are, by and large, surrounded by stretches of quiet downtime that make any individual fight feel like a scene out of an action movie.
RE: quantum mechanics: Likening it to nanomachines is unfair. Nanomachines in MGS4 were a lazy deus ex machine to tie up 20+ years of loose ends that were frankly unexplainable (or should've never been explained in the first place). Quantum mechanics, as used here, serve a real point, providing the framework for a very human tale, allowing us to see both the tragedy of man (Booker as he was, and Booker becoming Comstock) and the redemption of man (Booker choosing to drown at baptism). It also, in a larger sense, reflects the tragedy and redemption of America.
Not to mention, everything is foreshadowed. Quite cleverly, at that.