Tales of Destiny: Rutee in the original game. She's a Jerk with a Heart of GoldTsundereOnly in It for the Money with too much emphasis on the jerk part, too much story sympathy, and violent interactions with characters who don't deserve it. Added with the Die for Our Ship from Stahn/Leon fans, she's not well-liked at all, though her Jerkass tendencies were toned down in the remake, much like Leon's, and she shows remorse for some of her actions, like insulting Philia.
Many Tales of Vesperia fans look down on Karol and Estelle, claiming that they're a textbook idiotic Kid Hero and a textbook Na´ve Everygirl with less than stellar AI, respectively. They receive more character focus than some of the other characters in the party as well (Rita, Judith, and Raven), emphasizing their Scrappyness for their haters.
Sodia. Most of the fandom seriously dislikes her for her holier-than-thou attitude, Clingy Jealous Girl tendencies, and her attempted murder of Yuri.
Also, a lot of players were quite unimpressed with the Big Bad, because it turns out to be Duke. This is because his villainy comes out of nowhere and his motivations are poorly explained, which is especially bad in a series famed for its sympathetic treatment of villains.
Colette in the first game was also infamously bashed back in the day for constantly apologizing, her occasional Damsel in Distress tendencies, her "tripping plot power" being used constantly to resolve plot problems, and for the game forcing Lloyd/Colette on the player a little too much (especially for those who ship Lloyd/Sheena). The hate has certainly died down, and more people are voicing a liking to her, but the hate shall never be forgotten.
As for Tales of the Abyss, Anise gets scrappy points for her involvment in Ion's death and being forced to be a mole by Mohs. Did I mention Anise was clearly in love with Ion? Also, she gets additional scrappy points for being too Easily Forgiven for her transgressions compared to what Luke goes through after his screwup.
Nanaly is also a Tier-Induced Scrappy in her original game, because her arrows are utterly useless and hard to hit with compared to fast melee and hard-hitting magic, and without abusing a glitch in the PS2 version she only has one hi-ougi whereas other characters have four or five each. It's very rare to see her used after Harold, the most powerful spellcaster in the game, joins the party. Odd, as in terms of characterization she's an Ensemble Darkhorse, and if you take account her other appearances like in Tales of the World or Tales of Versus, she's an absolute beast when the game engine from her home series did not bog her down.