So, this topic has spoilers for everything. I won't mark them. You've been warned.
First off, I want to say that I loved the game, and I enjoyed the story. The story is not what I wanted, and that's ok. I'm a bit bummed about it right now, but I'll get over it. I just want to mention a few of the themes and ideas the story presents and then doesn't explore on a deep level, something that I would have loved. I am a student of American politics, and some of the issues which are part of the games setting would have been fun to explore. But they aren't. I'll elaborate.
The original Bioshock was about the setting. Rapture was a city founded on an idea, and idea which eventually tore it apart. Columbia is exactly the same, a city founded on an idea (Side note: that ending means so much right here!) Columbia is a city founded on the idea of America. American exceptionalism is the defining philosophy of the city. Columbia is American Exceptionalism taken to its most extreme level, the results being the worship of our founding fathers, preservation of extreme ideas (racial purity), and demonizing of those who would do away with that extremism (Abraham Lincoln). These religious ideas lead the city to rally behind their prophet and secede from "the so-called union," the "Sodom below" to preserve their vision of America.
This idea is ABSOLUTELY AMAZING. Going into infinite, I didn't really know that they created a fictional American Exceptionalist religion. When I entered Columbia, I was blown away. The idea was so cool. I'm very interested in (and critical of) American Exceptionalism. (Furthermore an American religion which probably inspired Levine's fictional one has played a big role in my life, Mormonism, but that is less important). I thought that this was an interesting worst-case scenario of American Exceptionalism, in the same way that the original game is an Ayn Rand worst case scenario.
I would have loved it if the game explored the evils of American Exceptionalism. It doesn't. It showcases it, and then changes subjects. Maybe we see how the idea can be intolerant and lead to violence, but the game never goes further than that.
Why didn't the writers see fit to describe a conflict between Columbia and the United States? Why didn't they go deeper into the motivation for secession? Why didn't they expound the radical doctrine of Comstock? These, and so many more ideas, would have been so interesting. There were so many ideas that would have made for a good story, but they didn't use them.
Again, I liked the game and the story, so I'll get over it. I'm just a bit bummed that the game created the perfect setting for a story about American Exceptionalism, and then went in a totally different direction.