I'm only posting the ones relevant to Optimus, but if anyone wants quotes (Starscream, Megatron), just haggle me. Will be edited as I will keep adding quotes.
Wars had a way of creating paradoxes like that. It could make enemies of brothers, murderers of lovers, heroes of the insignificant and cowards of the mighty."
-Alpha Trion
"Now a Cybertronian like Orion Pax would not go to the stars. He would not fight nobly for the ideals of the Primes. A Cybertronian like Orion Pax would monitor, assess and catalogue transmissions on the Grid because that is what Cybertronians of his caste did."
"Who was this Megatronus, this gladiator thug, killer of criminals and criminal himself, who gave voice to a longing that Orion Pax had never known he felt."
Orion: 'He' answered.
Jazz: 'He' being this Megatron, I take it. What did you say to him?
Orion: That he had more of an audience that he might have expected.
Jazz: And what did he say?
Orion: He said, "You are more right than you know. I am also more right than I know."
Orion: Who is us?
Megatron: Whoever we want to be. When you're taking on the world, you can't be choosy about who wants to be on your side.
Orion: So you have followers in Kaon. Where else?
Megatron: That's the kind of question a spy would ask.
Orion: If you're worried about that, we would have stopped talking long ago.
Megatron: Perhaps, perhaps not. Soundwave said I should worry that you will betray me. I say back to him, that if I thought you were going to betray me, I would meet you in the Arena and settle things like warriors. Would you fight me for your principles, librarian? Can you tell your principles from mine?
Orion: I think I can. And I would fight anyone for them.
"Hearing Megatron speak had lit a fire inside him that was not Megatron's fire but Orion Pax's. It was as if his Spark had never come to its full brightness until it had struck against the revolutionary ideas of this criminal gladiator."
Orion: Did I tell you that Megatron said he'd fight me if he thought I was going to betray him?
Jazz: Very funny.
Orion: He did.
Jazz: Then watch your back. If he brought that up, he's already half convinced it will eventually happen.
Orion: [laughs] I better get practicing and learn how to fight.
Orion: I don't think armed insurgence is going to be necessary.
Megatron: Maybe that's what it looks like from Iacon.
Orion: It does. You came up through the gladiator ranks. Every problem looks to you like it can be solved by fighting.
Megatron: And every problem looks to you like it can be solved by reading.
"Megatron leaned close to Orion Pax as the chant washed over them. 'Soon they will chant your name too,' he said. 'As long as they hold true to the ideals,' said Orion Pax, ' they can chant whatever they want to.'"
"'Autobots' he said finally, 'For we seek autonomy and see it as our basic right.'"
Orion: I have to return to Iacon.
Megatron: Do not leave angry, brother. What has happened was the will of Primus - else it would have happened. We are the vessels of our Creator's will, are we not?
Orion: We have our own will. The code of Primus is what guides us to know when we should and should not exercise it.
Megatron: We are friends. We will do great things together. But we must also realize that once we set events in motion, they will not always unfold accordingly. That too, is the nature of free will, is it not?
Megatron: Might be some competition there.
Orion: Competition for a hardened survivor of Kaon? Surely none of us weak, soft Iaconians would have a prayer against the scourge of the Badlands.
Megatron: Oh ho, his sense of humour returns!
"For a moment Orion Pax considered the irony. Megatron accused him of thinking and not feeling. Alpha Trion accused him of feeling and not thinking. Perhaps, he mused, this meant he had found - or was finding - some correct middle ground."
Megatron: If their deaths mean we get a hearing before the High Council instead of an all out civil war, then in the future we will know it was a worthwhile sacrifice.
Orion: But it's not a sacrifice they chose, Megatron. Isn't this all about self-determination? It's a little too easy for you to sacrifice other people for your goals.
Megatron: ... Yes, brother. Perhaps it is. This is one reason that I am glad for your friendship. You keep me conscious of these things that otherwise are too easy for me to forget.
"Optimus was gifted with extraordinary acute optics"
"Optimus had known Megatron for a long, long time. His former friend turned dire adversary was a skilled liar, but Megatron was not lying about this."
"Never let courage be the enemy of reason."
"Jazz had to talk and he had to complain. That was all right. It balanced off Optimus's own tendency to take everything too seriously."
Jazz: I don't see any other Prime but you.
Optimus: Jazz. I can tell when Megatron is lying. He wasn't lying.
Jazz: Maybe you're not as good as reading him as you thought.
Optimus: ... No. He believed what he said to me.
Alpha Trion: I watched you for a long time, Optimus Prime. I have seen the way you handle Megatron and the way you considered every idea from every angle. Yours is the kind of leadership Cybertron needs.
Optimus: I'm not sure of that. Where has it gotten us?
Alpha Trion: Where would we be if you had not taken the lead?
"'Check on Jazz.' Optimus Prime ordered. He wanted to do it himself; Jazz was his oldest friend and Optimus could not imagine life without him. But he was Prime and he had responsibilities."
"He had made all of his subordinates angry. Either that meant he was a good leader because he was not playing favourites, or he was a terrible leader because he did not understand their needs."
Megatron: You, brother - Orion Pax who now calls himself Optimus Prime - you lead your Autobots away. Who is the one who doesn't believe in the individual now? Most of Cybertron wants the Decepticon way. They want my way, brother.
Jazz: I mean, the Thirteen are a myth, O.P., they never existed. They're principles to guide us, you know? They don't have to be real for us to learn from them.
Optimus: I don't believe that.
Jazz: You don't have to. True things stay true whether you believe in them or not.
Megatron: Brother.
Optimus: Odd that you still call me brother. Your accommodations have been anything but brotherly.
Megatron: Family relations are always the most difficult.
"Megatron, thought Optimus Prime, you betray your true colours. Now that Cybertron could have been yours - a sickened Cybertron, inconstant upheaval, perilous to any and all life on its surface, but still yours - you throw it away to pursue a grudge."
Megatron: We will always be brothers. We are bound together. You cannot escape me, brother. I will hound you across the stars if I must, until every star in the galaxy has burned itself into a cinder. I will hunt you, and I will find you, and when I find you, [clenches his fist] I will, as I promised, see what the Core might have sequestered inside the body of the so-called Prime.
Optimus: Hunt me then, brother-if your hunt means Cybertron will escape your madness.