Let me first state that I thoroughly enjoyed the game. I started on Hard difficulty and was challenged in all of the places that you would think. Despite the title of this post I am ok with the fiction that is presented at the end of Infinite. Going through the game a second time and listening to the spoilercast gave me a few extra things to think about and the concept of an infinite number of stories works for me.
My disappointment in the ending of the game comes from a compliment I want to give the rest of the game. They did an excellent job of making me emotionally invested in the relationship between DeWitt and Elizabeth. I have tried to think of other times that I was so invested in a character or even the events of a story. Shadow of the Colossus comes to mind, but I'm confident there are better examples. Elizabeth never was a burden, and they did such a fantastic job moving her emotionally from the girl who twirls at the thought of a Paris to the woman who wants to end suffering that I jumped on that wagon as well. Towards the end of the game, after all of the savage Vox Populi attacks on the city, after they tortured Elizabeth and I rescued her again, all I wanted to do was get her to safety. I wanted to end the Chaos that the game had clearly descended into with the Founder-headed people in the asylum. I felt like the game had built to a wonderful crescendo.
But then the story took a turn and changed the meaning of the game to the metaverse and broad concepts of what "Bioshock" is as a story. I found that interesting, and although it felt like a distraction from the broader story I thought we were moving in the right (for me) when we learned that Anna/Elizabeth was DeWitt's child. The broad story arc of protecting and saving Elizabeth fit well into that. Then it became about how DeWitt is Comstock just before the game ended.
Playing the original Bioshock was about Rapture (at least to me). Trying to understand the city, it's players and how everything went down. Infinite stopped being about Columbia as soon as you go through the first tear (I believe Brad pointed out this in the spoilercast) your understanding of what makes Columbia interesting fades. You struggle to understand how this Columbia is different from the last but then you jump again and at that point it is no longer about the city. That works just fine, because (unlike the original Bioshock) it is now about the girl. But then at the very end the story doesn't deliver on the new paradigm.
So my beef with the ending is that while Bioshock was about a man and a city (that lighthouse thing is bullshit in my opinion), Infinite was about a man and a woman. At least it was through all of the game, but then in the end it decides to be about a commentary on infinite possibilities and doesn't close the chapter opened by your journey with Elizabeth.
Great game. Good mechanics. Fucking excellent story, but while the ending closes the story told by the Bioshock franchise (I agree they can't really make another one that is a worthy heir) it doesn't close the story presented in the game.