nonsensical ending
The big problem I have is how Booker 'takes over' his previous self at the baptism, where he is drowned. This is ridiculous, too much of a stretch, and as far as know totally unexplained. Booker didn't take over Comstock when going into his universe, even though they are the same person. So why did this happen? As far as I can see, the same Booker that we played as, the one that never went ahead with the baptism in the first place of course, eventually gets killed at the end at the 'baptism'. And of course this isn't the Booker they want to kill to rid of Comstock.
I suppose I should just accept 'it's what happens' when you go through the lighthouse doors, but come on... if things aren't explained properly then this is just nonsense!