The Faction System
The faction system was set up in order to eradicate the negativity, violence, and hatred in human nature. The people who established it had faith that in a society like this, humanity would be able to rediscover the virtues necessary for a peaceful, productive society. In reality, though, the faction system created bigger divides between people, and only fueled the greedy, power-hungry fire in people like Jeanine. Though it began with an admirable ideal, in many ways the faction system worsened the conditions of the people within because it taught them that only one virtue is important, and those who cultivate all the others are seen as an outgroup.
The Divergent
As readers learn at the very end of the novel, it is exceedingly ironic that the Divergent were the very purpose of this society, and yet they have come to be alienated and hated like outcasts. The Divergent are being hunted down and exterminated, and people like Shauna are afraid of them, even though the existence of these people is exactly what Edith Prior and her team were aiming for. A lot had to go wrong in this society for the perspective on Divergent people to shift so drastically from what it was meant to be.
Tobias's Weakness
Tobias's weakness ultimately was not one of his four fears, like readers expected. Tobias's true weakness was the faith he had in his mother, and his need for a familial connection that was so powerful it overrode his rationality. It was easy for Tris to see that Evelyn was using Tobias as a means to an end; Tobias is just as perceptive as Tris, so if he had been fully rational he would have been able to see this. Instead, though, he blindly did everything she asked of him, and realized only at the end what she had been doing—true to his character, though, he recognized his weakness and did what he could to atone for his mistake.
Peter
Peter has always been Tris's sworn enemy, right from the very moment that she first stepped into the Dauntless compound. The hatred Tris and Peter had previously felt for each other sets up for the extremely ironic and powerful moment when Peter is the one who saves her from the execution table, who replaces the death serum with one that would merely paralyze her. There is more to Peter than everyone believes.
