Young Justice did this with the Aqualad mantle by replacing Garth, a character widely mocked for having the same "useless" powers as Aquaman and wearing ridiculous short-shorts, with Kaldur'ahm, an Atlantean child soldier and magician who can create weaponry from water and generate powerful electrical blasts.
Their Garth isn't too bad either; he's actually more advanced in magic than Kaldur, due to the latter spending time on the surface world as a superhero sidekick. He also briefly demonstrated the "power of the Tempest", as an homage to his modern comic book identity.
The show in general has a habit of turning various villains into righteous badasses, even those who were pretty good before. Mister Twister was suddenly a huge threat, and Clayface (not an unpopular villain before) became downright terrifying.
Their take on Apache Chief also adds a lot of Character Depth. It gives him a Disappeared Dad, implies he doesn't get along with his mother's boyfriend, and is one of Blue Beetle's best friends before they both got superpowers. They also gave a more interesting twist to his powers: rather than simply growing, he surrounds his body with a huge human-shaped forcefield.
Apache Chief, Samurai, and El Dorado all get much more interesting characters and badass points here. The whole group turned into Ensemble Darkhorses post their first episode with lines, "The Runaways". Except for Static, who already had his own TV show and fanbase.
Speaking of Scrappy-Doo, they tried to change him during the "All-New Scooby and Scrappy-Doo" and the "New Scooby-Doo Mysteries": "Scrappy is now even more matured, and softened down from before, having a much bigger sense of danger. He will even back down if a monster growls loud enough, and can even be seen shivering in fear and crying for help; unthinkable in his earlier life. He is now the 'new Freddy', solving the mystery with Daphne, while Shaggy and Scooby return to their prior role as the comedy relief who only keep the ghosts busy while Scrappy and Daphne find the clues." ...sadly, hardly any of this showed up on the screen, and he remains The Scrappy to this day.
Aloha, Scooby Doo is practically a manifesto on rescuing Daphne from the Scrappy Heap. She dons a midriff-baring version of her traditional outfit - when she isn't just wearing a bikini - and the plot hinges on the world-class surfing abilities◊ you probably didn't know she had (it's not like it would have come up often).
Similarly, Ben's canon love interest Julie Yamamoto was initially hated by fans for being considered as a Satellite Love Interest who had been created just for the sake of giving Ben a girlfriend, having no real personality or interesting power and being considered as a Replacement Scrappy for Ben's crush in the original series, Kai Green (despite Kai appearing in only one episode of the original show and not being that popular). As the series went on however, Julie Took a Level in Badass by gaining a Galvanic Mecamorph pet named Ship who could turn into a ship and later a Powered Armor for her, and eventually learnt how to fight. Now she still has some haters, but also some fans, and most of her haters tend to be those shipping Bevin (Ben/Kevin) or Bwen (Ben/Gwen).
Jury Rigg was originally written off for being too similar in use to the more popular Grey Matter. Omniverse gave him a complete redesign, including an aviator's outfit, more hyper personality, and increased emphasis on his ability to build. He's now considered one of the more unique aliens in Ben's arsenal.
Dil and Kimi, despite being loathed Scrappies in Rugrats, were actually quite liked when they became preteens in All Grown Up!. Although some argue that Kimi's personality took a turn for the worse.
Brian Griffin was The Scrappy from 2009 to 2012, until the writers decided to kill him off. Now he's the most popular character on the show.
A really weird example with Meg. Early in the show, she was not a very well-liked character and was just an "average teenage girl" and didn't really do a lot of interesting things. The creators of the show took this and decided to make her a Butt Monkey, since people already disliked the character and it would give her more of a place and identity on the show. Ironically, the Butt Monkey status has really saved her with some of the fans: now people feel SORRY for her, and they cheer every time the creators give her some moments of happiness, like getting a good boyfriend or getting revenge on someone who was mean to her.
Spyke did appear in the comics as a member of the X-Force (which later became X-Statix)...although as canon immigrants go, this wasn't a very good one; Comic Spike was a beefy, arrogant adult instead of a wiry, carefree teenager. They didn't even have the same real name...but the inspiration, at least, was clear.
He sort of appeared in Black Panther going by the name David Evan Munroe (Spyke's name was Evan Daniels). He's Storm's younger relative like in the show, but so far he's too young to display any mutant abilites. At the very least, like Spike, the inspiration is clear.
His appearance in Final Wars also helped, where he acted like a true kaiju and decimated Sydney, Australia by himself.
It also counted as a Take That, Scrappy!. Once the "real" Big G showed up in Sydney, Zilla came charging in like a maniac for what looked like would be a battle of a Lightning Bruiser vs. Mighty Glacier. Nope; Godzilla smacks his CGI counterpart away with his tail - taking out the Opera House at the same time - and with one big Atomic Breath attack annihilates him. At least it was funny!
It has to be pointed out, the American Godzilla from the movies and the one from the cartoons are distinct, individual characters. Zilla remains a scrappy in the eyes of many fans, as his appearance in Final Wars demonstrates. But his son, Zilla Jr., is well accepted as a Kaiju on his own right.
A controversial example would be Lisa Simpson. Some have always loved her, while others think she became a Scrappy in the middle seasons (seasons 11-14), once she turned from The Smart Guy into a Soapbox Sadie. For the latter group, the show's last few seasons should seem like a good example of this trope. Starting from season 15, the show has had an unwritten ban on stories where Lisa gets involved in politics, in favor of returning her to her roots as a socially isolated smart girl.
Some believe this transition occurred twice. In the earliest points of the show, Lisa existed as either a blander Karma Houdini version of Bart or a Rightly Self-RighteousOnly Sane Man, thus making her occasionally insufferable. After the first couple of seasons however, Lisa developed a more pompous buffoonish side, more frequently humbled after being treated as an annoyance or displaying Not So Different tendencies regarding her family.
Owen from Total Drama Island, possibly. Season 2, he became an out-and-out Creator's Pet, by losing challenges while his team still loved him, winning them based on his farting and obesity, and being even more of a Gasshole. Not only did every character (including Chris) love him, but he got to return, to the joy of all the "good" characters, and make it to the final four. However, season 3 he's been toned down considerably: getting an actually funny sub-plot of being afraid of flying, and both negatively and positively contributing to his team. And his Odd Friendship with Noah and his breakup with Izzy.
Sierra has always been and remains a Base Breaker, but even many detractors will admit that she's more tolerable in the last few episodes of season three, when some quick and long-needed Character Development has her finally realize that she should treat Cody more like a friend than a prize to be won.
Scott has gotten this as of Season 5 to an amazing degree; he went from one of the most hated contestants to one of the most beloved. The reason for this is that he has stopped throwing challenges, started a sweet relationship with Courtney, and has had some funny moments. The fact that his Butt Monkey status has been upped considerably also gives him more sympathy from the fans.
Ahsoka Tano. It's generally been accepted that she started to get better as a character in Season 2 once they pulled back from having her in nearly every episode. As of Season 3 and several episodes later, it's safe to say Ahsoka has become a good example of a character being rescued from the Scrappy Heap. The good blood Ashley Eckstein has built up in the fanbase thanks to Her Universe probably helped a little, too.
Anakin from the Clone Wars (CGI) series is arguably his best characterization. He went from a character fans blame for ruining Darth Vader filled with endless Wangst to an actually likeable character.
They made Jar Jar Binks tolerable (and also gave him a useful ability)! One thing that helped here was they showed how other characters were sometimes annoyed by him, and how even his friends like Padme often are humoring him. Also, only one episode had him being ridiculously clumsy. And instead of inexplicably taking out tanks, like in Episode I, it just enabled him to dodge insanely well which, added to his cloak, made the Too Dumb to Live mooks assume he was a Jedi. He then used the fact that they thought he was a Jedi to trick them. That's right. Jar-Jar pulled one over on the bad guys. Summon Bigger Fish becoming an ascended meme during his first episode didn't hurt either.
Bucky Buenaventura spent the first season of The Zeta Project as an insufferable little borderline sociopath. He reappears in Season 2 with a flattering redesign, a new voice actor, a reasonable grasp of common sense and friendship, and a mild (and hilarious) crush on Ro, but keeps the mad hacking skills and snarky dialogue. The overall result takes him from horrendous brat to surprisingly likable lancer.
Sandy Cheeks of SpongeBob SquarePants began as a somewhat grating God-Mode Sue and near incorruptibleOnly Sane Man for the other far more flawed cast members. Following the second season however, the show began to lampshade Sandy's somewhat excessive talents and also developsomevalidflaws for the character (episodes such as "Pressure" and "SpongeBob, Sandy and the Worm" seemed to focus largely how Sandy wasn't good at everything). Ironically she is arguably the one main character in the newer episodes that hasn't had her callous or idiotic habits heavily Flanderized.
Nabu from Winx Club wasn't a very popular character when he was first introduced in season 3. Understandable, seeing as he was introduced late into that season, didn't get much Character Development and it was pretty obvious that he was just there to give Layla a love interest. He didn't even appear in the first movie apart from a brief cameo appearance at the very end. Season 4 gave him some more Character Development and some chances to show off his awesome magical fighting skills, which quickly helped make him a lot more popular. There's also Roxy, who was introduced in that season. At first the fans were a bit skeptical to her as they felt a seventh fairy wasn't necessary, but as the season progressed the fans seemed to warm up to her as she became more confident with being a fairy.
Cubert from Futurama lost his oft-annoying skepticism at the end of his debut episode.
Notably the creators had intended him as a parody of annoying characters (particularly Wesley Crusher), so even that episode had plenty of Take That, Scrappy! moments.
By the same token, the show continues the trend in spin-off media of distancing Iron Man from his "Nazi" Civil War persona by toning down his Jerkass tendencies and making him an anti-authoritarianrebel who tells Nick Fury where to get off and refuses to trust or cooperate with SHIELD.
Ignoring the comics, Maria Hill gained some haters for acting like a Jerkass after becoming director of SHIELD. In particular, even though she constantly needed the Avengers' help in saving the day, and needed rescuing by Iron Man at least once, she refused to thank them, because they fight crime as vigilantes. However, she gained some fans during the climax of the show's Secret Invasion adaptation, when she outsmarted the Skrulls invading the Helicarrier, then saved Nick Fury and Iron Man from the Skrull queen.
Thundercats 2011 made Snarf bearable by making him a Ridiculously Cute Critter who can't talk. The Thunderkittens have also received this treatment; it helps that they're voiced by actual children this time.
Transformers Prime goes Up to Eleven with this, by rescuing the human species from the scrappy heap. Unlike most Transformers shows, the humans don't suck this time. Agent Fowler is a Reasonable Authority Figure, the kids stay out of the way (as a group, individually is another story), and human villain Silas is just as threatening as any Decepticon. Only Miko is the typical Scrappy human, though she gets better in the second season when she becomes less prone to rushing into situations that put everyone in peril and starts to contribute more to the team.
A pattern started by Transformers Animated, which had a larger but still well-liked cast of humans. Several human villains appeared in the earlier episodes, but their presence was mitigated by the fact that they were explicitly intended to create a sort-of Sorting Algorithm of Evil with the Decepticons at the top; and when the Autobot/Decepticon conflict took the fore as the series progressed, the human villains faded quietly away. Ironically, though, the character who was probably the best-received human sidekick yet, Sari Sumdac, turned out to not be a human at all!
Human villain Meltdown was generally well-received by the fanbase, however, and got to appear the most during the first two seasons. Probably helped by him being a credible threat and all-around nasty piece of work compared to the others who - barring maybe the Headmaster - were usually an enormous joke.
The Headmaster probably got a huge boost to popularity because he took off Sentinel Prime's head in one episode which allowed Optimus to get some hillarious catharsis over on him
On the other hand, anybody who actually liked Lola for her personality and not just her curves can't stand the new Lola.
Irving from Phineas and Ferb, though never technically an official Scrappy, was definitely a Base Breaker: Half the fans hated him, the other half related to him and liked him. After his first appearance, though, he was given more Character Development beyond just being the Loony Fan that follows the boys around, and fans are now much more agreeing and accepting of him.
More specifically, Angel Bunny is starting to receive this treatment. He'd always been a bit of a jerkass, but the way he took it Up to Eleven in 'Putting Your Hoof Down" made many members of the fanbase despise him. A couple of episodes since then have portrayed him in a much more likable light. His heroic role in the 23rd issue of the comics (and the fact that he'll never get any recognition for it) seemed to have completely rescued him.
The episode "Baby Cakes" even managed to do this to baby ponies for some people. For a long time, they were a popular target due to their oddly anthropomorphic shapes arguably ruining the appeal of ponies. Then this episode used their similarities to real human babies to advance a meaningful plot.
Princess Cadance was a Base Breaker after her introduction in the season two finale, "A Canterlot Wedding," with some fans feeling she was a step backwards to the franchise's previous, more stereotypically girly generations due to being a literally pink princess whose special power was love. Being introduced entirely out of the blue with a minor helping of Remember the New Guy in a two-part episode revolving entirely around her wedding, and having been replaced by an evil shapeshifter until the last 10 minutes of the second episode didn't help matters. This dissenting faction quickly changed their tune after the season three two-part opener, "The Crystal Empire," when she helped thwart the villain by having her husband pick her up and throw her off a tower at him because she was too sick to fly under her own power.
Upon her introduction Babs Seed was not a liked character in the least. She came off as something of a sociopath with the way she bullied the Cutie Mark Crusaders far beyond what the other two bullies ever did which her Freudian Excuse hardly came close to justifying, and many fans thought at the very least she could have careened off that cliff and ended up in the mud before her Heel-Face Turn. However, fast-forward only four episodes and she was portrayed in a far more likeable light as a very lovable character, gaining her a ton of popularity. Helping further is her reappearance in an issue of the comics where she is able to bond with fellow reformed antagonist Trixie and helps her catch a jewel thief who framed her.
Lemongrab 2 was at first as hated as his brother. However, he too was rescued from the scrappy heap after the events of the episode Too Old. When the original Lemongrab became a cruel dictator, Lemongrab 2 became nicer and outright defied his brother (an example was when Lemongrab stated that something was unacceptable and he countered saying it was acceptable). When Finn and PB were escaping with Lemongrab's son Lemonhope, Lemongrab 2 gets out of the original Lemongrab's stomach and helps his son to escape. Because of his treachery, he was killed but not before giving Lemonhope encouraging words.
The Twins in Superjail started as the most hated characters in the show and were often cited as one of its flaws by fans and critics alike. The reasons given for hating them amounted to their voices being obnoxious, them ruining Warden's plans and seemingly only existing to do so, and them being a little too flamboyant for some fans' comfort. By the time of Season 2, they had gained their own following of fans and their focus episodes served to flesh them out slightly more. These days, the two are more of a Base Breaker as some still consider them to ruin the show, yet they have a lot more fans due to the revelation that they're the lesser-desired and bullied sons in their family.
The Mistress received Scrappy treatment from a periphery demographic of fans who felt she was getting in the way of Warden's relationship with Stingray, as well as those that hated her aggressive personality and considered her to not have as much interesting qualities as her male counterpart. By season 3, this died down a little bit, as she was revealed to be longing for one good man, and wound up sleeping with Alice, which seems to have (momentarily) killed the assumed threat of her getting in the way of shipping.
Wendy Testaburger had long taken heat from South Park fans for various reasons, whether it was her jealousy-filled murder of a teacher she assumed would take Stan away from her, her being annoying and a Soapbox Sadie, or the general shallow and on-and-off type of relationship she and Stan had (of course, they are kids). In "Breast Cancer Episode Ever", she became largely relieved of her Scrappy status when she managed to beat up Cartman. However, she does continue to be a base-breaking character as some felt her victory was undeserved and that she only exists to "be mean" to Cartman.
While people still have problem with Spidey, he starts to get a bit more sympathy due to being the Butt Monkey for his team and actually acting like the Only Sane Man in some episodes.
Power Man was criticized as a Flat CharacterBig Guy, but his nightmare in "Strange" caused some to warm up to him, and his appearance in the next episode, "Awesome", further helped him out.
White Tiger, big time. Most fans saw her as the most obnoxious character after Nova for most of the show, but "Kraven the Hunter" gives her a very large Character Development, revealing her origin, and shows her actually expressing affection for Peter.
Surprisingly Korra herself suffers a case of this in Book 2. At the onset of the season she gained a lot of criticism for seemingly regressing in her Character Development from the previous season and actually becoming more hot headed and unreasonable then she was previously (to the point that many fans were happy she disappeared for an episode after being eaten by a dark spirt. After hearing Avatar Wan's story and regaining her memory in the Beginnings Two partner she became considerably more wiser and humble, apologising to Tenzin for her Jerkass treatment of him at the start of the season and thinking her decisions through much more carefully (it also probably helped that this coincided with Mako becoming the shows Scrappy again after restarting the Love Triangle subplot).
In season 1 all three of Tezin's children were hated for being seen as useless comedic relief and Kid-Appeal Character's, along with helping fuel the romance plot. While Ikki and Meelo are Base Breaker's, Jinora got rescued in season 2 and 3 after she received a bigger role in the plot and Took a Level in Badass.
Wendy from Gravity Falls was derided in season one for being a generic "cool teen" character who didn't fit well with the rest of the main characters. Season two fixed it by leaps and bounds, first by having her join Dipper and Mabel's adventures and prove a very effective part of the team, and then having her admit the cool teen thing is just a facade and she's actually constantly stressed out.