Ambassador Donnel Udina has an obnoxiously aristocratic voice, gets overly angry when talking to the Council, sidelines you when you're inconvenient, sells you out just to maintain public relations, and acts as an appeaser for the Citadel Council if he's selected to be the human representative. Mass Effect 3 manages to do some degree of rescuing, as he becomes significantly more sympathetic even when he's attempting a Cerberus coup.
Miranda Lawson of Mass Effect 2, though not a xenophobe like Ashley (she believes humanity should seek to emulate asari technology), she still fully supports a human supremacist organisation. While her upbringing makes it understandable that she is used to perfection in work, blaming Joker for the loss of the Normandy's crew, despite the fact that he's the only reason they still have the Normandy is still unreasonable. Also, her treatment of Jack simply annoyed some players.
Plus, the fact the game deliberately angles the camera to stare at her arse at several points (including once during a dialogue option, which by necessity lingers until the player chooses what to say next) irritated several players, especially straight females who felt it was a blatant attempt to pander to horny fratboys.
Jacob Taylor was mostly ignored by players in Mass Effect 2, being considered a bland Master of None with a shallow and cheesy romance route who refers to Shepard as "the prize". The Narm Charm of his romance route is actually the entire foundation of his fandom. Come Mass Effect 3, he's the only romanceable character in the series who actually cheats on Shepard. Knocking up another woman and not even trying to get in contact with Shepard in the six months she was incarcerated. This did not impress the fans, to say the least.
The other councilors get this to a certain degree, since they're very hesitant to believe Shepard, and offer very little help in dealing with Saren and the Reapers; their typical role in the plot is to deny you help when they aren't actively impeding your efforts. Others believe that it's hard for them to believe Shepard given the nature of his/her evidence, and are more sympathetic to them.
Kai Leng of Mass Effect 3. The hate comes from his Story-Driven Invulnerability, little character depth in-game, cheap tactics, cyberninja character design (described as a Capcom villain wannabe), and obnoxious bragging. The interrupt that lets you smash his sword and gut him like a fish is right up there with the 'Hug Tali' interrupt, in that nearly everyone takes it, even if they're not playing the alignment. Some even decry the existence of that interrupt in the first place, since it involves yet another instance of Kai Leng-induced Cutscene Incompetence in Shepard turning his/her back on a foe that is not confirmed to be dead. The fact that he was a major player in a wildly decried fourth EU novel before ME3's release lost what little fan support he had in his introduction in the third. He ate Anderson's cereal, for crying out loud.
Diana Allers of Mass Effect 3 seems to be getting quite a bit of hate for a variety of reasons. Her inclusion being considered blatant pandering to IGN (she's modeled after and voiced by one of their writers, Jessica Chobot), her Romance Sidequest (considered by many to be the most shallow in the series, and which does not even award the achievement), her bland voice acting, and feelings by many that they dedicated far more time to her, an extremely minor character, than other aspects of the game (many note more effort was put into sculpting her high-polycount ass than into Tali'Zorah's face). The fact that she replaced Emily Wong, a pre-established and well-liked character, did not ease the anger.
Morinth isn't too well liked as well, due to being a very vicious villain with little plot relevance whose only real purpose is for Samara to explain how Ardat-Yakshi work to you and to give you nightmares. Her status as a Scrappy is one of the few things fans on /v/ agrees on.
The kid seen at the beginning of Mass Effect 3. Partially because of his poor voice acting, partially because he is seen as a cheap Expy of Newt and his death is a blatant attempt to arouse sympathy, and partially because his model is purposefully used for the Catalyst.
Which brings us to The Catalyst, the one responsible for the Gainax Ending. Leviathan somewhat acknowledges this and the criticisms of the Catalyst's Insane Troll Logic. Its existence is foreshadowed by the Leviathan, a member of the species whom the Reapers were modelled after, who explains that the Reapers are being controlled by a fundamentally broken AI, trying its best to work on faulty programming.