Bianca also qualifies. During the Club Battle, she became a Scrappy for her love for Zorua. But once the episode with her father aired and she underwent Character Development, she is a Scrappy no more. It also help that she Took a Level in Badass.
Also, Nena Trinity once she killed an even bigger Scrappy than herself: Wang Lu Mei. Unfortunately, Nena wasn't able to do much of anything after being rescued from the heap, as she dies immediately afterwards.
She fares better overall in certain adaptations that alter her notorious Moral Event Horizon crossing to not be as bad: such as the manga where it actually is an accident (one she shrugs off and feels no remorse for, but still not deliberate) or in Super Robot Wars where all three Trinity siblings kill Louise's parents in attacking a political event under orders, rather than Nena attacking a wedding on a whim.
Mobile Suit Gundam AGE had Asem Asuno, the second generation protagonist. His angsting about not being an X-Rounder and his need to prove himself to his father did not do much to endear him to the fanbase. Then comes a Dying Speech from his mentor Woolf about walking his own path and becoming his own pilot, and Asem proceeds to kill Desil Galette, despite a total lack of Psychic Powers, a rarity for Gundam protagonists. To rephrase, he beat the series' Newtype-equivalent with NO special powers at all, just pure skill. Suddenly the fans are singing the praises of Asem Asuno, the SUPER PILOT! His becoming a Space Pirate with appropriately themed Gundam in the next season has only increased his Bad Ass, as far as the fans are concerned.
A rather odd example: Naruto's Sasuke has been considered a Scrappy for the longest time in America. But once he'd been pitted against Danzo, American fans have actually started rooting for him. Though this may be more because it's his Crowning Moment Of Awesome than him just being the lesser of two evils. Others root for Danzo instead, as they think he is making pretty good points and agree with his way to lead the village.
Also happened to Karin when Sasuke sacrificing her to kill Danzou turned her into The Woobie. Although she survived, she made it clear she didn't care about Sasuke after what he did. Not only did this remove her from the shipping equation, but she also displayed, what some fans believe, more common sense than other characters in the series. Although that fell flat when she reunites with Team Taka after that and easily forgives Sasuke after he just awkwardly mutters a "Sorry, Karin". While some found that hilarious, a lot of readers didn't take that well and quickly called her the most pathetic female character in the manga (which is saying something).
Sakura went through this at the start of Shippuden due to Character Development and becoming a lot stronger. She's been getting in and out of the pile from then on, but quickly became The Scrappy again in the Kage Summit arc, after her fake love confession to Naruto, her inability to kill the defected Sasuke and generally not doing anything besides crying and relying on Naruto again like in Part 1.
The real Madara Uchiha is more of a Base Breaker than a true scrappy because he does have his fans, but he won a LOT of nay-sayers over when he hijacks Obito's Rinne Tensei to revive himself instead of all the people that died during the Shinobi War, effectively killing off a much hated character, and single handedly preventing what many feel would have been an incredibly lame plot twist that would have rendered the last 100 chapters pointless. Unfortunately, he returned to scrappydom when he becomes a full blown Villain Stu.
Suzaku Kururugi from Code Geass, after Lelouch Geass-es him to "Live!", which causes him to revert from his fake (and debatably hypocritical) nice guy persona to his brash, rude, and brutally honest "true self".
Then we have Rolo Lamperouge, performing a heartwrenching Heroic Sacrifice in order to take Lelouch away from being shot by the Black Knights, killing himself in the process through Geass overuse.
Sakuno Ryuzaki from the animated version of The Prince of Tennis is portrayed as a "sweet and earnest, but klutzy and stuttering child", and thus, she's often reviled, hated and called "anti-feminist" and "stupid". But several Sakuno haters have come to like her better after reading the manga, which tones down her klutziness and makes her a pint-sized, more self-assured Yamato Nadeshiko. Same goes to her Chinese drama self, where Sakuno is somewhat more outspoken and independent and a promising artist on top of that.
Conversely, some fans (often of the Het is Ew type) dislike manga!Sakuno's portrayal as the ideal girlfriend for Ryoma (whom they see as a possible Purity Sue), but prefer her anime counterpart as the clumsiness and insecurity are semi-realistic character flaws.
The School Days manga portrays main character Makoto Itou as more sympathetic than his other versions (that of an idiotic jerkass who cares only about boning as many girls as possible). In the manga, he is portrayed as a well-intentioned idiot who actually cares for the girls, other than just schtupping them.
Sadly, the process was reversed with Sekai Saionji. While she's portrayed in games and anime as being impulsive and idiotic yet having a good heart and showing remorse for her actions, Sekai in the manga is shown as quite the self-centered and manipulative bitch... and two of the PlayStation endings definitely go this route as well, without giving her the madness excuse that Kotonoha tends to have when she goes Yandere.
Bat from Fist of the North Star went from annoying brat to capable warrior between the first and second series. He grew up pretty well.
Shiho is considerably more tolerable in Mai-Otome than her Mai-HiME counterpart was, since she doesn't spend her time watching over Yuuichi (a.k.a. Sir-Not-Appearing-In-This-Series) like a hawk, and actually gets to be her own character for a change. At the very least, the complaints about her whininess don't seem to be as loud with the new series. Although some still prefer her Mai-HiME self since she had more dramatic weight instead of being a Running Gag character.
Miaka Yuuki, main character of Fushigi Yuugi, appears to have gotten a little less flak from some of her haters thanks to Eikoden; their reasoning was that no matter how bad they thought Miaka was, she at least had good intentions and cared a lot for other people than herself, whereas Mayo was a hundred times worse.
The little duck billed bratty demon, Kanchome, of Zatch Bell!, was generally useful for little more than a random flawed disguise on the spot to help his True Companions, and his attitude had The Scrappy written all over it. The anime gave him a Crowning Moment Of Awesome by having him nearly defeat a stronger foe with a new spell that made replications of himself, but he would go on to be much more badass in the manga - he saved the Earth from destruction by Clear Note (the Big Bad) by transforming into the Earth and hypnotizing Clear to think it was the real thing.
Many a fan of Saint Seiya profoundly hates Seiya for only winning his fights due to support from others. His author, Masami Kurumada, seemed to get the message when he made Bt X, which features many expies from his previous works, as was his style. Seiya's expy Teppei, while still very brash and headstrong, has a strong resolve to stand on his own two feet and delivers. To make sure he didn't veer off too much in the opposite direction, however, he does see what happens when he ignores his B't when he nearly dies against the 5th Point Soldier, and a balance is struck. More than a few fans agree Teppei is much more likable.
Also, the fans seem a lot fonder to Seiya ever since his appearance in Saint Seiya Omega.
Chris Thorndyke from Sonic X, in the final two series, after being given a Plot-Relevant Age-Up and some actual abilities, plus being portrayed as being significantly less clingy and self absorbed.
Momo Hinamori from Bleach has finally gotten some bits of slack from the fanbase after her return to action, where she saves Matsumoto from Halibel's Amazon Brigadeand says that she's got things to do now, showing that she's starting to get over the massive trauma that the Soul Society arc was for her.
The Zanpakutou Filler arc rescues her further from the heap, whereas she starts taking active roles in battle and the arc actually shows that she is awesome on her own right.
And now, as of chapter 449 Orihime seems to be going in this direction, as she finally got her wish to be the Combat Medic and an active part of the True Companions, which has shut up a good part of her haters.
In One Piece, Usopp was heavily criticized by the fanbase for dueling Luffy and leaving the crew over Luffy's decision to replace the irreparable Going Merry, causing some of his detractors to bring up his relative weakness compared to the rest of the crew. Later in the arc, he adopted the persona of Sogeking to avoid getting a large bounty for attacking Enies Lobby as well as to prevent his former crewmates from noticing who he was, although only Luffy and Chopper didn't notice, and demonstrated a powerful new weapon with new techniques and far greater accuracy. Then he later apologized for his actions and rejoined the crew. Considering how Oda seems to work, he had probably planned the story that way all along.
It also helped that the duel itself was fantastic, as it showed that Usopp was more than a Lethal Joke Character, to the point where he could actually go toe-to-toe with Luffy.
Bellamy. Prior to the Time Skip, he was just an arrogant dick that none of the fans liked, not helped by the fact he was a poor fighter who Luffy beat with one punch and without his devil fruit powers. Post-Time Skip, he reappears in the Dressrosa arc, matured, respectful, and his fighting abilities significantly improved, along with some depth in his devotion to Doflamingo. Thanks to this Character Development, he's started getting a bit of a following and is certainly no longer The Scrappy anymore.
Koizumi Kyoko from 20th Century Boys is first presented as an overtly comedic Butt Monkey akin to Heckel from Monster, and just as out of place. However, once she gets sent to Friend Land and becomes more involved in the central story, she becomes quite sympathetic and one of the characters the audience can most identify with, as a regular person thrown into the center of an epic battle against an evil conspiracy.
Higurashi no Naku Koro ni's Chew Toy, the sometimes annoying crybaby Satoko, gained a fanbase after standing up to Shion while being stabbed to death. In some fan's eyes, Takano Miyo's flashback arc did a great job at making her sympathetic and cheer-worthy in the eyes of a lot of fans, even though she's the Big Bad.
Raki from Claymore, post time-skip. From a whiny little "protect her" obsessed powerless crybaby to... THAT. There should be a limit to these things. He manages to talk down a medieval angry mob, smiling all the way, and (to put it in perspective,) he's holding himself off from awakening due to the death pikes harder than one of the female hybrid Claymores, which actually managed to turn the second strongest Claymore into a cat-monster-thing with no resemblance to a mind. Think about that. Although it's been implied that it's not due to him, but to...something...on his back.
Asuka was widely hated during the series run. She was a total bitch for no reason (To the viewers) and was just a horrible character. Then came the Mind Rape and the genuinely tragic Freudian Excuse. It drove some people to like her. Then came the rest of her story in the anime, and she gained more fans. Then came her LastStand against the Mass-Produced Evas, where she is horribly mangled in the cruelest evangelion death to ever be in the franchise, and the rest of End of Evangelion where Rei and Shinji trigger the Third Impact (because Rei was unsure on what to do so she asked Shinji) and everyone else's actions in the movie (Ritsuko dying, Gendo dying, Misato trying to help Shinji but failing and dying, etc. etc.).
And if somehow you still dislike her, the manga adaptation and the Rebuild of Evangelion movies even moreso tones her down into a more likeable Jerk with a Heart of GoldTsundere, so her actions in the anime are absolved by a few more people.
Soul Eater: This, apparently, was the effect for some of Mosquito's Bishonen Line during the Baba Yaga arc. He was dead within two chapters - interrupted transformations sequences FTW.
This good-looking younger version of Mosquito is the one he uses to slice Death the Kid's arm off. This is an Evil Is Sexy thing, isn't it? Had he done it in his massive gorilla-insect-ish forms, people wouldn't have 'Rescued' him.
Crow Hogan, from Yu-Gi-Oh! 5Ds, may be on his way to this. His being a signer is slowly being justified, starting with the acquisition of his Dragon, and in later episodes, he actually has been sidelined in favor of other major characters.
White was initially bashed for not being anAction Girl, but she's getting major sympathy points as she fell out of the Nimbasa Ferris Wheel due to the shock of her Tepig, Gigi, abandoning her for N. It helps that she's also resolved to become an Action Girl after the incident, steadily becoming stronger as a character now that she's recovered from her Heroic BSOD.
Axis Powers Hetalia: Sealand became a more liked character after his role in the Hetalia Bloodbath 2010 strips. Additionally, Korea and Japan appear to have become less hated with the passage of time: the ugly incident regarding real-life Korean Moral Guardians is hardly ever brought up against Korea now due to it having faded away into the past, and Japan having a minor role at best in the most recent webcomic strips have put a damper on accusations of him being a Spotlight-Stealing Squad or Relationship Sue.
Elizabeth Middleford of Black Butler in chapter 57. This sweet, adorable and harmless Damsel in Distress reveals herself as a Badass Adorable in Chapter 57 and confesses that she desperately wanted for her fiancé Ciel to not see her "uncute" side, and deliberately hid her badass side up until then. Even nearly at the cost of her own life. Shortly after Ciel berates her for such behavior (Prioritizing lady-manners over survival), when she is about to die while Ciel, who despite his best efforts ends up injured and unable to save her, is in danger, Elizabeth spontaneously leaps into action and stabs down the zombies using swords in both hands. While tearfully declaring that she'll protect him, even.
During her first arc in The World God Only Knows, Kanon Nakagawa drew a lot of hate for being a YandereAttention Whore. Her later role in the story shows her softer, much more likable side, and the fandom has mostly warmed up to her.
Ishigaki, of Majin Tantei Nougami Neuro, started out as an annoying and mostly ignored assistant for Detective Sasazuka and was at the bottom of most popularity polls. He ultimately seemed useless and even the series said so. However, after an arc where he tries proving himself when a rival enters the case and his bizarre hobbies end up helping solve the crime while showing his amazing creativity and hilarious dark side, he shot all the way to number two on the next popularity poll, nearly beating Neuro himself!
Onpu from Ojamajo Doremi was very much disliked during the first season. She used magic to solve all of her problems and even used forbidden magic for trivial purposes such as getting her mother to take her out for dinner in order to avoid having to eat green peppers. Although she isn't entirely to blame for her misuse of magic when you consider who her teacher is. However, even without magic, she was still kind of a prick and speculated that the reason Tamaki never gets punished by her father is that he doesn't love her and says it out loud in Tamaki's face. She does get better near the end of the first season though as the last two times she used forbidden magic was to help another girl with her audition and to save the other girls from being turned into witch frogs. In season 2, she whole heartedly joined the other Ojamajos, and her popularity made a significant jump to the point where she was the only other Ojamajo Doremi character who made it very far in the fan-driven 2002 Anime Saimoe Tournament.
In Girls und Panzer, while Maho was not necessarily an unpopular character to begin with, some viewers had a negative first impression of her after her cold treatment of her younger sister Miho, but changed their mind after her Pet the Dog moments, and when Little Army revealed that her greatest desire and the reason why she serves as Nishizumi heiress is for Miho to be able to live her own way, which is why she adopts a Jerkass Façade.
Iona Hikara/Cure Fortune of Happiness Charge Pretty Cure was an unrelenting Jerk Ass towards Hime Shirayuki/Cure Princess due to Hime's Dark Secret of opening the Axia Box and releasing the Phantom Empire. When she revealed this point, she was still a Jerk Ass, but now it was Jerkass Has a Point. Two episodes after she revealed that to the rest of the cast, she suffers a Break the Badass moment as Precure Hunter Phantom beats her down and destroys her original powers before revealing that her real reason for revenge against him, her sister being captured, was all her fault. A few moments later, it's Hime leading a Big Damn Heroes moment to save Iona and give her the means to restore her powers. She mellows out considerably, especially after the next episode she learns that Hime was tricked into opening the box.
Ayumi Sakagami/Cure Echo of the Pretty Cure All Stars New Stage trilogy was a massive Base Breaker due to the fact that she essentially stole the first New Stage movie, with many fans feeling that her time should have been devoted to the past Cures instead (though many point out it wouldn't of saved the movie any more). This is made worse by the fact that, when she does become Cure Echo, she doesn't fight at all, only confronting Fu-chan before reverting back to normal. After being Put on a Bus for New Stage 2, she comes back for New Stage 3, becoming a more proper Pretty Cure, being able to actually help the other Cures and getting fairy partners of her own with New Stage 2's Gurell and Eren.