I thought the tie-back to Rapture was way cool, too.
I think the Elizabeths and our timeline Booker realized the only way to end the cycle was to kill him before he was born-again and turned on the road to becoming Comstock. Sorry if i'm repeating previous posts.
As i think about the Elizabeths popping out of our time-line, after Booker is drowned, it shows them breaking that cycle and having a different life. I don't think it means they "die", I think they escape what others have pointed out as a destiny scenario, somehow influenced or observed by the Lutece's.
I think the question is did the Elizabeth's drown Booker before or after he gave Anna to Lutece? If before, then it presumes an entirely different timeline for Anna and Booker. If after, then Comstock is never instantiated, but Booker has previously given Anna to Lutece. But Comstock was there when Booker did. Thus, a conundrum.
Anybody see something that breaks that constraint?