Just finished the game and absolutely adored the end-game, yet the only thing that's bothering me is why exactly Comstock became such a huge white supremist. If he was getting baptized to deal with his guilt for murdering so many people at Wounded Knee and then becomes a born-again Christain, why would he suddenly do a complete 180 on that issue if that's why he turned to religion in the first place?
Also I kept assuming Comstock wasn't so much a religious nutbag but rather a murderous conman before the plot-twist, since if he was the former I didn't really see how he could reconcile secretly murdering so many people if he did legitimately believe he was a holy prophet.
EDIT: Also while I dug Songbird I guess I could have gone for delving more into what he was exactly besides being the Columbia-version of Big Daddy. Similarly those weirdass bell-headed guys in Comstock's house near the end.