|Mordin: Old Blood|
Dealing with Maelon presented an ethical dilemma for me, especially considering the choice given to me on the Collector base. Do you keep the data from such horrific events, or do you deem it too tainted to be useful? On only one playthrough did I keep the Collector base in tact, but I was surprised that Mordin reacted in the way he did: he completely disapproved of my actions, despite the fact that we had done the very same thing with Maelon's data. Perhaps it was because he didn't trust the Illusive Man (a well-founded bias, I assure you), but it seemed inconsistent with his character.
Of course, Mordin is one of my favorite characters in the whole series; ultimately, it was him singing "Scientist Salarian" that cemented him on the list, but watching his character arc from his first appearance to his last, he's probably one of the more well-developed characters, connected not just to the main story but also to that of the krogan, my favorite species and subplot. And that arc truly did begin right here, shooting our way through the cavernous hospital on Tuchanka.
I haven't done this before, but hey, here are honorable mentions: Garrus and Legion.
* I guess you could count helping Wrex find his family armor and Garrus locate and kill Dr. Heart in the first game. Neither of those missions really change the story, as far as I can tell, though, except maybe when you confront Wrex on Virmire. Please correct me if I'm incorrect about this.