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.
The most hated character in Symphonia is easily Emil from Dawn of the New World... and he's the main character. To be fair, Emil's more of a case of Americans Hate Tingle (he still manages to rank very high in Japan popularitypolls) and the fact that his game came out right after Tales of Vesperia which introduced the badass of all badass Tales protagonists. In other words, Emil had a tough act to follow after what Yuri demonstrated in his game and didn't meet the expectations of the American fanbase.
Marta doesn't fare a whole lot better, due to coming off as overly fangirl-y and a bit whiny.
Colette was also infamously bashed back in the day for constantly apologizing, her occasional Damsel in Distress tendencies, 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.
Luke has a fair amount of hate, whether for being an arrogant Jerk Ass in the first part of the game who ends up getting manipulated into destroying a town and starting a war, or for being Wangsty in the last part of the game, after the Time Skip.
This Tumblr post goes to great length to analyze and defend Luke, however.
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.
Milla and Jude from Tales of Xillia get this at times for different, albeit related, reasons. Milla gets this for the massive amount of Character Shilling that happens for her in game, both as a result of her role in the plot and occasionally for no explicable reason whatsoever. (Wyverns bend knee to her, she can tolerate pain explicitly stated to be unbearable, almost every NPC is in awe of her etc.) This gets dialed Up to Eleven when she temporarily kicks the bucket and the party reacts like it's the death of the Messiah, going beyond even very serious grief and into a full-blown existential crisis. Jude gets the Scrappy treatment at times...for shilling as hard as possible for Milla.