SPOILERS! (duh)
I too am in the minority; I did not love Bioshock: Infinite. I enjoyed the game, but the story never grabbed me, and it wasn't because it didn't make sense or that my choices didn't matter.
No, my problem with Infinite is not a structural one, it's an artistic one.
When you first enter Columbia, the game makes an effort to affect a soothing atmosphere, to project an image of an ideal place, but the second I walked into that baptism, I knew exactly how this whole scene was going to play out.
Columbia is entrenched in American exceptionalism and traditionalism; two deeply flawed ideas. It comes as no surprise that such a place would carry within it all the negative connotations associated with those things. Being deeply oppressive and violently rigid is to be expected of a place that makes all of it's decisions based on religious conjecture.
So this begs another question; why would any sane person ever want to live here? Are people drawn here because they believe the quality of life is better? Are they taken by force? If we are meant to relate in some way to people within this tyrannical system that oppose it's values, we never get the chance because the only people who ever stand up to it are being oppressed by it.
This, I believe, forms Infinite's Achilles heel; the story has no point. The only people you can really relate to are Booker, Elizabeth and the Vox, but the problem with this is that none of those three ever do anything to distinguish their characters. The only reason you can relate to Booker is because he is self interested, you can only relate to Elizabeth because she experiences the setting in the same way you do (It's all new to her), and you can only relate to the Vox because they behave like an oppressed minority WOULD behave.
No meaning can be extracted from people doing exactly what you would expect them to do, there is nothing to learn here.
An example of how to do this right; Andrew Ryan. Unlike Columbia, Rapture was built on good intentions; the tragedy of Rapture is that you can sympathize with it's ideas, with it's concepts, with it's goals, but it is the indifferent an inescapable forces of human nature and entropy that destroy it.
Andrew Ryan has a unique and controversial perspective, but it is a legitimate perspective, that you could arrive at with logic and reason. Andrew Ryan is a tragic figure because he is a human one, and as horrific as Rapture was, there was once beauty in it.
Comstock and Columbia are nakedly awful things born of nothing but dogmatic psychosis. It is impossible to relate to this concept, to this idea, because it's the work of a cartoon character; nobody with a functioning brain and a grasp of badic ethics could ever build something like Columbia with sincerity. Perhaps there is mileage to be found in the idea of Comtock being INSINCERE, but this is never touched upon.
Columbia is just an awful place that collapses because (Surprise, surprise) people are not fond of being oppressed. There is no pathos, there is no real tragedy.
So, now to address the ending. In a word; So? I understand perfectly well the mechanics of what's going on with the split realities and such; I even predicted the ending as soon as we entered another reality. "The hero is secretly the villain" isn't a novel idea anymore, in fact, it's just the literal manifestation of the metaphorical "Fighting with monsters" trope, which is older than dirt.
But I will not criticize the game for not surprising me, a good story does not need to be unpredictable. Instead I will ask this; what is the point of Booker being Comstock? What narrative or metaphorical purpose does it serve? The obvious one would be implying that the two of them aren't so different, but since neither of them are fully developed characters, this means nothing. Not to mention that I don't buy that the Booker we spend most of the game with, who reacts to almost nothing other than Elizabeth in any meaningful way, would have the intelligence, charisma or desire to found a national hate group; what few basic personality traits Booker and Comstock have, they do not have in common.
So the idea that Booker might have become Comstock means nothing, because we have no sufficient explanation for how this happened. Oh, we're TOLD that it was a result of wounded knee, but again, Booker does not have definitive enough personality to contextualize these events.
So I will ask again; what is the point of the alternate reality plot? We only ever visit two or three different realities, so it isn't really used as a narrative or framing device, and it doesn't lend the story or characters any depth. I get the impression that it's just in the game because it's unusual and bizarre.
Bioshock Infinite spends so much time just explaining how it's sci-fi twist works, that it forgets to ever make it's existence meaningful. Would it have not been more interesting to, say, see Booker become more like Comstock in real time; to see his philosophy and psychology shift and evolve; to see him actually become the villain, instead of the game just telling us he is.
Infinite seems like it's banking on just the existence of it's final twist to be so amazing that the wow factor alone will justify it's inclusion. But Bioshock Infinite spends the majority of it's time with Booker and Elizabeth trying to escape from Columbia, and that journey is sorely lacking in the areas that really make a story great; it's theme is non-existent, it's characters are nothing special, and it's plot is merely unusual.
I enjoyed the game, overall; the polish and presentation of Infinite are nothing short of fantastic, and I don't think it's entirely lacking in substance, but I do find it severely overrated and nowhere near as profound as many people make it out to be.