Mystique: Kurt, people have hated you your whole life. Why do you fight for them?
Nightcrawler: I fight for the ones that don't.
This exchange between Tony Stark and WarMachine in the latter's deploy in SpecOps 7 Mission 1:
War Machine: [returning from a deploy] All set, Tony. I hit the kill switch on that little operation.
Tony Stark: I knew I could count on you. You're so trustworthy you make me feel bad about myself.
War Machine: Oh, good. It's working.
This exchange between Tony and Rescue when the latter took to the field:
Rescue: Glad you're with me, Agent. Let's try to keep collateral damage to a minimum.
Tony Stark: Worry about yourself, Pepper. I can build another tower, I can't build another you.
From Spec Ops 14:
Thor: Agent. Together we will face the Destroyer yet once more. I have come to think of you as my talisman against it. To battle!
From Season 2, chapter 3. If Jean loses the heroic battle Xavier and Magneto give Jean a motivational speech.
In Season 2, Chapter 2, Agent Hill warned Rogue against going into a combat situation without back-up, but Rogue brushed her off thoughtlessly. In Special Ops 16, this reckless tendency gets Rogue captured by the enemy. It's a testament to Maria's professionalism that she does not use the opportunity to say "I told you so," but instead works to rescue her almost as hard as Gambit does.
Agent Hill: Let's move, team. Rogue's in trouble.
Season 2 Chapter 1 Mission 3, if you lose Heroic Battle (which requires Nightcrawler) against Mystique, she will say this to her son to prove that Even Evil Has Loved Ones: "Come back, my son. Come back. We don't have to fight any more."
Molly Hayes joining the Avengers. The girl's intro speech shows that she's absolutely thrilled to be there.
Even though the rest of the team is concerned, especially her father and husband, Betty Ross is actually thrilled to be able to join the team as Red She-Hulk. Not only is it nice to see Red Hulk and Hulk agreeing on something, but seeing Betty's enthusiasm is sweet too.
The message◊ thanking the players after the game's closure was announced.