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.
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.
The original Mobile Suit Gundam meanwhile had Kai Shiden, a self-professed coward with the face of a thug and a brash personality. While he does get some Character Development over the course of the show, it's not until Mobile Suit Zeta Gundam, wherein he reemerges as the UC equivalent of James Bond, and a number of sidestories that he becomes a veritable badass in his own right.
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 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. Sadly, she 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. However, her Cool Big Sis role around both Naruto and Hinata during The Last and overall supporting them does genuinely managed to regains some of her former glory that she once had at the start of Shippuden. Unfortunately it also didn't last for too long, and she ultimately becomes a major Base Breaker as of Naruto Gaiden.
Elfen Lied: Bandou came across as a Scrappy because, despite being a badass, he was also an unlikeable, obnoxious one-note character who merely enjoyed killing and was intent on getting Lucy. Even when he became a Handicapped Badass, his rather stale portrayal left people wanting more. Then Bandou began to interact more with Mayu and proved to be intelligent, as well as being a badass, by daily cleaning garbage from the beach to prevent Lucy's extensive arms to throw them as projectiles and showed a Jerk with a Heart of Gold side to himself. It also helped that Bandou proved to be one of the more realistic, gray-scaled characters in a series that was more inclined to show everyone to be jerks.
Suzaku Kururugi from Code Geass, after Lelouch Geass-es him to "Live!", which causes him to revert from his fake (and debatedly 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 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 B't 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.
Bleach During the Training from Hell segment of the Bount arc, Lirin's smug demeanor and grating laugh (in addition to the grating length of that segment itself) made her almost insufferable. After she officially joined the team, she becomes much more tolerable.
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: When They Cry'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.
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! 5D's, 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.
His ARC-V incarnation is widely praised by most fans for his role and lack of focus, especially in the first half of the Synchro arc.
Emerald is generally the least-liked Dex Holder in Pokémon Special, but his Back Story gave him Woobie status. His new appearance in the ORAS chapter has also been better received, as he now has his hair down and ditched his fake limbs.
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 B.S.O.D..
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.
Similarly, the Student Council received a negative first impression for essentially blackmailing Miho into doing tankery again. Then it's revealed that they have to win the tournament or else the school will shut down, and shortly after this revelation, Anzu takes a more active role in her tank, which becomes much more effective as a result.
Anzio wasn't as well liked as the other schools at first, since their battle happened offscreen in the anime, and while Anchovy appeared in the manga, not everyone liked her looking down on Miho for sacrificing victory to save the flag tank. In the Anzio OVA, Anchovy's quite competitive, but significantly nicer, holding a meal for her team, Miho's team and the support staff after the battle.
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.
Attack on Titan: Historia, after several chapters of cooperating with her father and seemingly working against the Survey Corps was increasingly loathed by many fans, reaching peak contempt when it looked like she was going to eat Eren. Then she turned on her father and freed Eren, redeeming her in the eyes of many.
Jellal was a fairly controversial character pre-Time Skip, due to perceived overexposure (especially with a lookalike) and controversy over whether or not amnesia pardons his past actions. Post Time Skip, between his self-punishment over what turned out to be brainwashing and pretty much canonizing Jerza, he's now a fairly popular character.
While Sting good side was showing a few chapters prior, Chapter 300 might have had him join Rogue in being the only well-liked members of Sabertooth after blasting a hole through Jiemma after obliterating Lector for showing he had a guild mark. The fans were pleased to see Jiemma get it coming. Rogue and Yukino have been getting a lot of love, too, after the Grand Magic Games arc, especially following the Sabertooth side-story.
Also, Flare was a disliked member of the disliked Raven Tail guild...until said guild disbanded and she came to Lucy and the rest of Fairy Tail in an apologetic state. When her backstory and Freudian Excuse for her prior behavior came out, the hate for her pretty much vanished in-story and out of it.
Though she remains a Base Breaker by and large, Minerva, of all people, has surprisingly ascended to this trope to a fair degree. Before she was one of the most reviled characters of the story, but after it was revealed she is the way she is due to her Abusive Dad (who, among other acts, beat her for crying and left her naked in a forest one night, and even demands her to kill a fellow guild member!! And when she refuses, kills him himself!!) and that she actually regrets what she had become, the fanbase eased up on her a little bit. Obviously she still has a lot of things to make up for, but as far as most readers are concerned, this is still tremendous progress in her development. And then there's the aforementioned Sabertooth side-story.
Koujirou Shinomiya of Shokugeki no Soma garnered plenty of hate in his introduction for being portrayed as a Bad BossJerkass alumnus who was deliberately setting up students to failure during training camp, but became much more likable when his motivations and why he's so judgmental were revealed. As the series progressed, Character Development started to kick in as he looks towards achieving a new goal rather than staying stagnant in the past with his culinary skills. He's become so popular he consistently ranks in the top ten for favorite character polls, even garnering a Spin-Off series detailing on his culinary career post-graduation.
Also, Erina who was previously seen as Soma's Jerk Sue rival. To many fans she was cruel, condescending, and simply unpleasant. Her haters started to find her more sympathetic thanks to Characterization Marches On to Defrosting Ice Queen, her friendship with Hisako, the anime showing more of her Adorkable moments and her Up to ElevenJerkass father returning to Tootsuki, who was responsible for her bitchy behavior to begin with, and showing that she and Alice truly love each other, despite their differences.
As of the last few years the Lyrical Nanoha series has actually gone a long way to making Precia Testarossa a much more sympathetic Tragic Villain. When she was introduced in the shows first season she was hated pretty much instantly thanks to her first scene wherein she was shown horrifically whippingFate while the latter was tied up for not collecting enough Jewel Seeds. This hatred only increased when she revealed to Fate at the end of the season that she was just a clone of Precia's daughter Alicia and that she had always hated Fate. The fact that she ended up (presumably) falling to her death instead of having a fight with any of the main protagonists also left a bad taste in a lot of viewers mouths with many fans hoping she would return just so she could get the ass kicking she deserved. However with the release of the first movie fans actually got to see a more sympathetic side to Precia seeing her hold Alicia's lifeless corpse in her hands and realising as she fell to her death that she could have treated Fate like an actual daughter instead of a tool. This continued in Gears of Destiny wherein she reconciles with her familiar Linith at the end of there arc as the two die peacefully in each others arms. Finally we have INNOCENT wherein Precia becomes a Doting mother to both Alicia and Fate (as well as being funny to boot). Suffice it to say these portrayals have gone a lone way to making Preica much more sympathetic in the fandoms eyes (it properly helps that audiences were introduced to the much more universally reviled Hückebein about the same time).