The Divergent trilogy is full of symbolism. Sometimes it works rather nicely, and other times it feels like overkill. Well, here's a symbol that captures my reading experience of Allegiant:
Everyone has probably experienced that immense level of frustration of trying to load a webpage, and when nothing happens you refresh the page over and over again and never get anywhere. Ultimately, you become so irritated you either give up, or you need to reboot your computer because it stalled.
My reading experience of Allegiant was similar. The story is bogged down by endless chapters of philosophical debates on nature v. nurture, then the plot abruptly shifts to an action or romance scene, and then it regresses back to an endless philosophical debate that accomplishes nothing. The "divergent" characters should immediately grasp that it isn't one or the other, but they don't.
The whole nature/nurture discussion also doesn't adequately address why Tris's divergence is so profound compared to the rest of humanity. Any miniscule amount of scientific research will show the explanation for Tris's divergence is impossible.(show spoiler)
The entire reasoning we're given about divergence fails miserably.
My negative reaction has more to do with the story as a whole than its conclusion. The plot was sloppy, and I also had a difficult time distinguishing between Tris and Tobias's narrations. It's hard to believe the author's editors/publicists/agent let such glaring problems slide.
I don't think the ending Roth chose was unfounded given Tris's behavior in previous books, but it's not what I wanted for either Tris or Four. When an author takes readers on a journey and asks them to suspend a great deal of logic, then they will expect a payoff. We weren't really given that in Allegiant. I applaud the attempt at a bittersweet ending, but I don't think Roth successfully pulled it off.
If you're interested in hearing the author's perspective about the book's conclusion, she wrote a post about it on her blog.