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Similarly, Dynasty Warriors: Gundam 2 nods to Lacus' Hatedom by having a non-canon storyline where she really does turn out to be an evil, manipulative queen-bitch who hops into a Gundam and kicks her own boyfriend's ass after he realizes the truth.
Flay Allster suffers from this a lot. While she isn't exactly innocent in canon (she does go Yandere for a while), there are reasons for her Sanity Slippage, mostly how she witnessed her father getting blown up. A stunning number of Alternate Universe and High School A.U. fics, which don't feature Flay's traumatic experience or the existence of Coordinators (thereby removing the Fantastic Racism), nonetheless decide to make her a monster. She's invariably the bitchy, spoiled, jealous and unfaithful girlfriend that Kira is dating at the fic's beginning solely so that he can break up with her to be with Lacus (or Athrun). She always goes out of her way to pick on Lacus, and does her best to make all the characters miserable, for absolutely no reason. Even the kindest and most forgiving characters will feel nothing but scorn for her, and of course she feels nothing but hatred for them (as a being of pure evil, she can't feel love). Needless to say, Flay's canonicalredemption will be completely ignored.
A parody of such a trope is Kira Yamato himself in one Japanese Gundam flash animation site in which Dearka Elsman becomes a hero against the "evil Kira". Normally known as a sincerely good-hearted, peace-loving hero, in this animated short he is altered as one such trope due to the fact he pilots Gundams terribly well.
Protagonists such as Amuro Ray and Kamille Bidan have been victims to this trope, too, due to their apparently unlikeable initial personalities, as compared to the Draco in Leather Pants villains Char Aznable and Haman Karn, who, in the eyes of fans, can absolutely can do no wrong.
Even if you ignore the Die for Our Ship, plenty of fans hate Relena because they think she's a useless idiot who detracts from the plot by opposing the war, and is unrealistically naive by believing in peace and pacifism. Never mind that Gundam is and always has been anti-war, Relena arguably does more to resolve the main plot than the Gundam Pilots and demonstrates a good deal of intelligence and savvy despite only being 15 during the TV show and 16 in The Movie.
Quatre does have issues—probably more than Trowa, really, because as the end of the above post indicates he believes killing is bad even when necessary and yet also believes that it is required and acceptable for him to do it under the circumstances. He's set himself up to be Hitokiri Battousai, except he's smart enough at least not to put himself and his machine into the hands of any one faction. He has not made the transition to being a killer as smoothly as he probably needs to; the other idealists among the pilots have solid warrior mentalities to fall back on. But he does not have the kind of issues he's given in such stories.
However he's the only one who had that level of issues with the mind-warping ZERO system, probably because of his inner conflict as well as all the crap he got put through while flying it. Heero and Duo coped better, Trowa is Trowa, and Wu-Fei just used it to go on a Vision Quest. ZERO told him to work with the other pilots. So he did.
Marina Ismail, another Expy of Relena Peacecraft, is given similar treatment. Although a devoted total pacifist and a symbol of the fainting good in humans, so many fans tend to hate her for excuses such as being a totally useless, indecisive Mary Sue. Even her heart-touching song, Tomorrow, does not help.
Flit Asuno is getting some of this treatment after the timeskip. While it is true that he Took a Level in Jerkass and that his way of dealing with Yurin's death is unhealthy and sending him Jumping Off the Slippery Slope, bear in mind that the girl was a possible Love Interest was brutally murdered in front of his own eyes by Desil, an Ax-CrazyEnfante Terrible, and that he's seen many civilians (including his own mom) slaughtered by the Vagan army, so he's got some pretty good reasons to hate them. But tell that to the Misaimed Fandom who, after the reveal that the Vagan were Human All Along, seems to have forgotten the atrocities their military pulled. (The non-military people... well, that's something else.)
In canon, he kind of doesn't help his case. Even Kio and Asemu get tired of his genocidal attitude after encountering Vagan civilians or meeting sympathetic members of Vagan's military. To Flit for most of the show, he wants to wipe them all out and become a 'savior'. It took Kio bringing Yurin's spirit back from the dead to remind him what being an actual savior IS and save the Vagan's Second Moon from self-destruction.