After quite a few playthrough, I have begun to notice how Shepard sometimes adressess the vs differently. Such as how they say their name in the intro when they first meet each other in ME3, one sounding more 'oh, it's you. :I' and the other sounding more 'gasp, it's you!

'. It's also in the way they say 'thanks' when they get picked by the normandy after. Also, how they talk in the mars mission, in which they sometime's sound like old friends who might become more, or people who used to be sortof friends but now has serious trust issues.
None but one of the Shepards I played romance them in previous games, but the unromanced Shep's responses stilll differed, so it's not only the romance that affects how you speak to them....
So I'm not sure what triggers the different dialogues. Is this affected by how intimate you were in ME1(not counting romance), as to say how much you talked and how how nice you were to them? Is there actually flags for how nice you were?