More or less everyone except for Garrus, Tali, and Liara suffered.
Miranda as I felt she was the strongest romance for Shepard and yet she is barely present, even though Cerberus is at the center of all the conflict in ME3. I would have preferred her replacing Ashley given the latter didn't offer anything this game.
Ashley got a ridiculous makeover turning from the girl next door to a trophy wife (what happened to her chest?) and then was absent half of the game and didn't offer anything after being recruited unless you had romanced her.
I really do feel bad for all the FemSheps who romanced Jacob and then he was forced with another women, even having a child! Why not place him with Kasumi at least?
I really wanted Kelly to have a larger role instead of her few lines of dialogue on the Citadel. Traynor was okay, but came across as being fan service for FemSheps. She didn't really seem to add anything else otherwise.
All the news reporters (besides Alers) seemed to have been written off without much of a presence.
Kal'reeger had an underwhelming end via mail. So did Rana Thanoptis. What was the point of having her in ME1 and ME2 if she was just gong to be written off in ME3?
Doctor Chakwas had no role at all as well as the engineers.
It was clear ME3 was too ambitious in scope and so there was a lot of fan service and nods, but very little substance for most of the companions in the previous games, especially ME2.