Couple more observations:
Notice that in the after-ending credits, Booker's apartment still looks like shit with empty alcohol bottles laying around. Doesn't even seem like a great father.
Also, Rapture was built in the mid-40s, so the lighthouse analogy isn't constrained by time. As long as there is a "man, a city, and a lighthouse".
I don't think we'll see anymore Bioshock games out of Irrational. This game pretty much explains how that entire universe works.