Guess I'll bite... Yeah it's kinda long, feel free to read or TL:DR :P
I really like the ending and the overall story in the game. Part of what I really enjoy about the story and the ending is that it's open to alternate interpretations. The conclusion to the story can be seen and interpreted in quite a few different ways. That someone is unclear or left partially unexplained does not make it a plot hole. This is something often seen in books or movies but not really something that's been explored a lot in games. There are some examples (Journey is one that springs to mind), but it's the first time I've seen it in a really high budget large scale game.
Some general observations:
A general theme of the game is religion. I think a way to look at both the story in general and the ending in particular is to look at it through a religious lens rather than a scientific point of view.
Consider that in Christian tradition, baptism is a spiritual rebirth. This is also brought up in game where Comstock talks about baptism, claiming that the person going into the water is not the same person that comes out. Other religious themes are the idea of rebirth, forgiveness from past sins and redemption. All themes are a very relevant to Bookers character, all themes he struggles with or longs for in some form.
During the ending, I don't think booker is killed by Elizabeth in a physical sense, he is pushed under the water and he passes out, just like he did when he was baptized when first entering Columbia. At the end Booker wants to kill all the different Comcast's, Elizabeth at this point really steps into her role as a 'prophet or Jesus figure. Instead of bookers idea of killing, she gives booker a rebirth, she frees him for the past and the sins, the chains and the dilemmas that comes with them. At the very end, after the credits, Booker wakes up again in his room with a baby crying in the next room. This to me insinuates that 1) He was not killed by Elizabeth 2) That he has been given a second chance, he can right the wrong by never giving away his child. 3) It raises the question if he'll actually be able to take advantage of this second chance or if it's all really in vain, perhaps he'll fail again. That's something left up to the players to ponder. That, in my mind, is the true ending: For all his travels, in the end his reward is a chance at redemption and a second chance to do right by his child.
Another religious aspect is that of Elizabeth. She is a pretty obvious allegory for Jesus. She is prophesized to be a religious leader, she has miracles powers, she's very good, kind and innocent and in the end, it's the very religious that wants to put her on a pedestal that also seeks to corrupt her and hurt her until she becomes a twisted instrument for war and death.
The religious angle goes a lot further, the game contains a very strong indictment of religion. Both the obvious with Comstock as a clearly religious and evil figure, but also the Luteces who can be seen as abusing other people's faith. For example, when Comstock talks about seeing an angle after Wounded Knee who tells him that he will build Columbia, I believe that is Lutece doing the talking. She tells him that he will build Columbia, she knows that he will because she's also the one who invents it and makes it happen. She's the one who makes him a cult leader by 'giving him' prophetic powers. Her ability to look into the future through, allows her to create the illusion of miraculous powers in the eyes of the population. When Comcast needs an hair and a prophet, she's the one who makes it happen by pulling the baby from another time and place.
Another facet is the nature of selfish choices as opposed to acting for the common good. The Lutece 'twins' represent this. It's implied (as least I see it as such) that the two Lutece are not twins, but rather the same person from two different worlds. For the sister, 'he' is the perfect companion. For the lone, misunderstood genius with no one who understands her and few who accepts the idea of a woman as a superior intellect, the twin represents someone who understand, someone who doesn't judge, someone who shares her ideas. However by pulling him into her world she might well be the cause of the whole mess. She creates Comcast, Columbia and the machines to realize her dream and in the end the consequence of her getting her perfect twin is that the world will ultimately burn. There's a couple of Vox's that explains that the twins are in disagreement of what they should do. That one of the would rather let the world burn then give up the twin, whereas the other is wanting to part ways in order to resolve the problem they've created.
Other areas that you could look at is the way the game looks at american exceptionalism, the relationship between oppressor and the oppressed.
The bottom line? The game is often vague and unclear, but it also leaves a lot of room for interpretation, discussion, thought and debate. That, in my opinion, is what makes Infinites story pretty awesome.
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