Jessie, James, and Meowth. Though they're not without their sympathetic qualities, many fans ignore their clearly unsympathetic actions, like trying to steal a 10-year-old's best friend, trying to kill people who get in their way, harming or even attempting to kill Pokémon who've pissed them off (they nearly killed the Squirtle Squad with homemade bombs and they clearly weren't planning on letting the Scythers who gave Jessie a new haircut walk away), trying to kill a 10-year-old on several occasions, etc.
Before Gary’s Heel–Face Turn when he was still a jerkass, fans tended to take his side over Ash during the Kanto/Johto arc of the show by justifying his jerkass behavior towards the latter. This is due to the fact that Gary was always one step ahead of Ash. This is also because he was a well skilled trainer that earned 10 badges while Ash didn’t earn 4 of the 8 badges that he had correctly. While Ash had his flaws, fans are ignoring the fact that Gary was much more arrogant and rude than Ash ever was in the series and that Gary was knocked out of the Kanto League earlier than Ash was. This has become less of an issue later on, since Gary has become more of a likable character.
Paul is easily the least sympathetic of Ash's rivals, releasing any Pokémon that don't meet his standards, insulting Ash at any given opportunity and acting cold toward everyone else he meets, and most notably having his entire team gang up on his Chimchar in an effort to force it into activating its Blaze ability (which is unusually powerful) and then rage-quitting on it and releasing it, effectively abandoning it out of disgust (everything that happened that day and the night before really soured Ash's opinion of Paul). Despite his jerkassery, he has a sizable fanbase on account of the excellent quality of his battles, high count of Jerkass Has a Point moments across the series, and Character Development similar to Silver by the end, to the point where he's part of a fairly popular ship with Dawn.
Harley is often softened up because he's extremely popular and over-the-top, to the point that James even said he wore leather pants in the PUSA Dub. His sheer flamboyancy garners him quite a fanbase, even if in-universe, most attempts at being pleasant are purely manipulation to fulfill his vindictive (and hard-to-define) obsession with destroying a ten-year-old girl.
Georgia is less drastic of an example since she's only a rival who engages in petty squabbles with Iris (and she admittedly does get better later in the series). Fans do, however, tend to defend her rude behavior towards not only Iris, but to everyone else on the show. This mainly seems to be because she was the only character that actually managed to put Iris in her place for her own condescending attitude, even turning Iris's trademark "such a kid" insult against her. They tend to forget that Georgia acts more immature and practices poor sportsmanship, and that her role is The Rival in the series.
Video Games
Cyrus from Pokémon Diamond and Pearl/Platinum has quite the fanbase due to his sympathetic backstory... despite the fact that he tries to destroy the universe and re-shape it using a Legendary Pokemon (Either Dialga, Palkia, or both depending on which version you get) so that he can basically become God. In Pokémon: Diamond and Pearl Adventure! he manages to redeem himself, starting from when the hero shows compassion towards him. This series is hugely popular among his fans and Team Galactic fans in general, partially for the more humanised view of the members, though even then it's made quite clear that they're wrong in what they're doing.
Silver, The Rival from the second generation, gets this a good bit too; he's easily the biggest asshole of the rivals in the series (what with Blue basically just being kind of a brat and petty bully, and the others all being friendly), between stealing from Elm, kicking/punching/shoving you in what is one of the only direct acts of violence from a human in the series, and infamously stripping you just when you were about to infiltrate a building infested with Team Rocket members, but yet he is one of the most popular and loved within the rivals. However, unlike some other examples it can be justified if the fanwork depicts him in the later parts of or after the events of the game, as he does get a Heel–Face Turn and majorly takes a level in kindness by the end. It helps that he has one of clearest character arcs and Character Development of any rival, especially in the remakes, where he has a Freudian Excuse in being Giovanni's abandoned son with a major Inferiority Superiority Complex thanks to it, acts like a Tsundere towards the end, becomes a borderline doting trainer and has nothing but humble respect for you by the end, has much more of a pretty boy look, and for the less emotional side of the fanbase, the fact that he's such a badass, that people tend to love him. It should be said that when he is discussed, even fans of him generally understand that he's an initially unrepentant JerkassHate Sink; they simply love that about him.
Generation I/III Blue sometimes gets this as well; while he isn't evil by any means, some, especially in the Japanese fanbase, make the mistake that relations between him and Red were perfectly peachy when manualsshow that to not be the case, or tone down his Jerkass qualities despite him being infamous for them. On the western side of things this can get particulary bad with people who believe that his Ratticate died on the S.S. Anne (some going as far as to give Red the Ron the Death Eater treatment), along with some people treating him as a bit of a Memetic Badass, probably in large part due to the reputation of his anime counterpart and being the Final Boss. His more mature Older and Wiser teenage self in the second generation and their remakes, and a Bishounen look in the latter (and to a lesser extent in the first generation remakes), do not help matters.
Giovanni himself gets this too, due to him being a rather handsome Yakuza/Mafia crime boss with nice clothes to boot. In the Japanese fandom this can be seen with the Rocket Executives as well; though they are still acknowledged as evil, they often get turned into more comical versions of themselves like a somewhat more competent version of the Team Rocket Trio, get their Undying Loyalty (especially Archer) to Giovanni played as a Tear Jerker, or both. Note that these are a bunch of Pokemon traffickers, thieves, and murderers, but damn if Archer isn't loyal to his former boss. This may be at least partially attributable to the anime due to aforementioned Terrible Trio.
N may not be a villain, but most fans forget that he was explicitly built up as the main antagonist in the first game, and intentionally antagonized the main character into conflict in most of their meetings. The fanbase's utter adoration and ignorance of his bad qualities, especially when Black and White was still new, is probably why Pokémon Adventures decided to make him muchlesssympathetic and amp up the "Jerkass" in Jerkass Woobie. However, unlike many other examples and similarly to Silver above, this isn't without basis in canon due to most if not all of his bad actions purely being the result of him being misguided by Ghetsis and his Ambiguous Innocence, with it being shown that the man only ever had good intentions, and by the end of his Character Development he becomes much more of a straight-up hero.
Lysandre sometimes gets this as well; it is not uncommon for fans to downplay his actions, even depict him hanging around with the main characters, despite the man being completely Zubatshit insane.
Volo unsurprisingly gets this. Despite being an unrepentant villain on the level of Ghetsis, he's attractive, perky and assisted the protagonist when they were banished from Jubilife Village. Most fans tend to gloss over that he's just manipulating the protagonist and depict him hanging with them legitimately, often with his evil aspects removed.
Kieran's fanbase tends to paint him as either a naive kid who had no idea what he was doing (partially true, in the sense that he was naive, a child and way over his head, but it's also clear that his cruelty was deliberate), or as someone whose negative actions were all the result of an outside force (namely the previously-leaked Pecharunt) corrupting him (which is never confirmed anywhere in the DLC).
Pecharunt itself ended up getting this treatment when its lore video was released. The story revealed Pecharunt's sympathetic backstory, which led some to believe Pecharunt was actually a sweet Pokemon that went bad because its adoptive parents spoiled/abused it. This is ignoring the fact that the reason its adoptive parents started making constant demands of it was because Pecharunt itself brainwashed them and amplified their greed, all in the hopes of receiving more of the love it was already getting from them. And this is without mentioning how the story has a few discrepancies that make it hard to tell just how much of it we're supposed to believe.
