"They each have an equal role in government; they each feel equally responsible." […] "I think it's unsustainable." (2.85-2.86)
Early on, the choice is presented between an equal government and a government in which certain factions, like Dauntless, have more power than others. The irony is that Tobias finds the first kind of government beautiful, even though that's exactly what he goes against in the end. And Tris, who thinks equal government is unsustainable, succeeds in demolishing the government altogether.
My instinct was to believe Marcus, and I usually trust my instincts. (3.72)
Tris's main conflict of loyalty is between Tobias and Marcus, who is Tobias's abusive father. There's something in her gut telling her to trust her boyfriend's sketchy father. Needless to say, this doesn't make Tobias happy, and she has to decide who to believe in.
"Evelyn," Tobias says. "I chose Dauntless." "Choices can be made again." (8.103-8.104)
This whole faction system is surprisingly malleable. The society is supposed to be divided up into five different factions, but it seems that most people get to choose wherever they want to go and change their mind whenever they want to. Is this society more about taking choice away (and being really bad at it) or about giving people choices?
"I'd rather be factionless than Dauntless." (9.21)
Edward talks as if it's a choice to be factionless, but is it? It seems that for some Dauntless the "choice" is between exile and death. Is that really a choice, when you think about it?
"I was born for Abnegation. I was planning on leaving Dauntless, and becoming factionless. But then I met her, and… I felt like maybe I could make something more of my decision." (12.81)
Tobias's choice involves a little more than just choosing a faction or choosing to become factionless. He's choosing whether or not to stay with Tris, and he's trying to figure out what is best for both of them.
I remember Evelyn's voice, speaking in the shadows in the factionless safe house: "What I am suggesting is that you become important." (21.17)
Tobias has to make a choice between his nature, which is fairly compassionate and diplomatic, and acting the way his faction expects him to act: fearless, cruel, and violent. That's a choice that most people in this book probably have to make, but Tobias's choice is front and center, because he's being pushed by his mother to achieve a position of power.
By the time the fight dies down, my clothes are more paint-colored than black. I decide to keep the shirt to remind me why I chose Dauntless in the first place: not because they are perfect, but because they are alive. Because they are free. (24.56)
It's easy to forget that Tris has a choice when it comes to her faction. What does it say about her that she pretty much chooses to be alive? Would she be more suicidal if she chose a different faction, or less?
As Marlene and the other Dauntless girl step off the edge of the roof, I dive at Hector. (26.31)
Sometimes Tris has to make some difficult choices in an instant. This is literally a life-or-death decision she has to make. One person will live, and two will die. Why does Tris choose Hector over Marlene and no-name?
All I can do is decide if I trust Marcus or not. (38.3)
Near the end of the novel, we're brought back to this: will Tris choose her boyfriend (who, by the way, just said "I love you"), or will she choose her boyfriend's father, who might just be a dirty liar? This choice sets the final events of the book into motion, and even sets us up for the finale of the trilogy. It's not a small decision.
"It is not my wish to encourage division in this community, which has given so much to me," says Johanna. "But my conscience forces me to go against this decision. Anyone else whose conscience drives them toward the city is welcome to come with me." (39.156)
Okay, this decision is huge as well. Johanna is the leader of Amity, a faction that seems to pride itself on its ability to make unanimous decisions. What Johanna is doing is giving the members of the faction a choice. This choice might tear the entire faction apart, but Johanna does it for the same reason Tris makes her difficult choices: she thinks it's for the good of the entire city, not just her faction.