The Ace Attorney anime, while keeping the same story as the games, turns Morgan Fey into even more of a villain than she was in the games. In the "Reunion, than Turnabout" case in the game, Morgan is partnered with Ini Miney, cooperating with her to get Maya arrested for murder, while Ini simply wants to kill Dr. Grey to protect the secret that she is, in fact, Mimi Miney. However, in the anime, Ini doesn't want to kill Doctor Grey, she just wants to fake the channeling so he doesn't find out that secret. Morgan, however, comes up with the plan to kill Doctor Grey and frame Maya for it. When Ini refuses, Morgan threatens to reveal Ini's secret identity.
In the original Art of Fighting game, King was a reluctant Punch Clock Villain who gave Ryo and Robert information needed to rescue Yuri after being defeated, with her later appearances firmly establishing her as one of the good guys. In the anime film, she's an unambiguous villain and the one who actually kidnaps Yuri (at Mr. Big's behest) in the first place.
Annie Leonhart from Attack on Titan is a ruthless killer in both anime and manga, but the manga goes further to portray her Anti-Villain status, giving her more humanizing moments such as genuinely smiling at one point, mentoring Eren Jeager in hand-to-hand combat, and also looking visibly shaken when she accidentally kills civilians. All of these moments are removed from the anime while also increasing the number of people she kills. It's not unusual to hear people say they hate her after watching the anime, then they read the manga and start sympathizing with her.
The first anime of Black Butler does this with Queen Victoria, of all people. In the manga she's a straight Cool Old Lady though she seems to like the idea of a Zombie army, while in the anime she's responsible for Ciel's parents' deaths, and planning to start a world war to "cleanse" the world with her angelic accomplice, Ash. It is, at least, implied that she's not at all stable, in part due to Ash's machnations.
In the Bokurano manga, Koyemshi/Dung Beetle is quite a jerk throughout, but he has a few Pet the Dog moments, such as performing a Mercy Kill on his sister, Youko, and giving Ushiro reasons to fight. In the anime, he's significantly more vicious, including mocking one of the dead kids, was quite a Dirty Cowardwhile he was a human and ultimately gets killed by his aforementioned sister when he tries to force the youngest of the group into the game.
More like "Adaptational Antagonism", but Leon Mac Nicol in the Bubblegum Crisis OVA was supportive of the Knight Sabers, but much like George Stacy towards Spider-Man in relationship to their comic counterparts in The Amazing Spider-Man, Leon in the Tokyo 2040 remake considers the team vigilantes and a blight on the AD Police.
In the manga version of Chrono Crusade, Big Bad Aion is portrayed as misguided and possibly insane, but sympathetic, having turned to evil deeds in a desperate attempt to fix what he felt was a corrupted system after learning an Awful Truth. In the anime, he was turned into the literal Anti Christ.
Cross Marian of D.Gray-Man. In the manga, he was a victim of Jerkass Façade at best, or a Jerk with a Heart of Gold at worst. But the anime, done by TMS Entertainment, decided that they wanted him to be a complete Jerk Ass. Episode 27: My Master, General Cross is infamous for the villainization of Cross' character -when Allen begins to tell Lenalee tales of how horrible his master is, so she'll know what to expect when they find him. The includes things from Cross that actually contradicted his manga characterization and Word of God.
In the aforementioned episode, Cross is shown forcing Allen into slave labor to make money, whereas in the manga, Allen only gambled to make money. Also, in canon Allen mentioned he only gambled if he and Cross were very broke. But in the episode, Cross forces Allen to gamble and steals his money when he's living off of a rich lover at the time. Allen mentions that his master was lover to a Maharajah's widow because he has a thing for rich women. Word of God however, has stated that Cross likes good women, not rich women. We also see Cross telling Allen to bring him a lion, which almost gets Allen killed, in addition to throwing Allen to legions of Akuma without training him. And Allen mentions that given Cross' treatment of him, he battled with depression as a result, only finding happiness with Narain, a friend he met in India.
Filler episode 25 Allen is shown to have a severe mistrust of all Exorcist Generals -saying that due to his bad experience with Cross, he didn't believe Generals were good people. There was also a scene where Yeegar speaks to Allen about Cross, saying that he is the best at destroying Akuma, but isn't good at human interaction. Neither of these scenes were in the manga, and contradicted the canon of General Yeegar already being dead before Allen and Lenalee are sent to find Cross.
Changes were also made to canon scenes where Cross is shown doing things in them that weren't in the manga. Such as the guards dragging Allen out of Cross' room at HQ. In the manga, Cross just watches as Allen is taken away. However in the anime, he smirks and hums mockingly while waving Allen off. In addition to stealing food from the cart of the vendor he spoke to in Krory's village -which he wasn't shown doing in the manga.
In Hallow -the 2016 continuation, there were cases of scenes and lines being cut. In the manga, Cross hugs Allen, saying he wishes Nea had chosen another host as his vessel. Then he says he can't laugh at Tiedoll's open affection for his students in longer. He's also shown wondering is sacrificing one thing always has to be done to protect something else, which hints he sees it as a case of I Did What I Had to Do. In the anime, Cross just tells Allen he's going to kill someone he loves when he becomes the 14th. Hie 2 lines about Tiedoll and Dirty Business are complete skipped over.
Finally, both anime adaptations have a habit of changing Cross' facial expressions to include him smirking or scowling when he wasn't in the manga. One such example includes Hallow's episode 13, which adapts the flashback chapter 206, with Cross caring for young Allen. In the manga, toward the end, we see Cross sitting with Allen in the bedroom, and he has a sad expression on his face as he watches the traumatized Allen. In the anime's episode, Cross is shown watching Allen with a scowl on his face instead.◊
Dangan Ronpa 3 does this to Mukuro Ikusaba. Dangan Ronpa Zero and Dangan Ronpa If ended up having her be portrayed more sympathetic and she ended up performing a Heel–Face Turn in the latter work. Here, this show seems to downplay her sympathetic qualities and instead focuses a lot on the thoroughly reprehensible actions she committed as an accomplice in her sister's schemes. It is extremely noteworthy that she stated that Makoto Naegi (aka her crush and the person who was responsible for her Heel–Face Turn in Dangan Ronpa If) is a loser that is better off dead.
In the manga of Deadman Wonderland, the staff of the titular prison Hand Wave the prisoner deaths in the dog races by claiming that they are done with special effects. In the anime, the special effects angle is done away with; and the prison openly admits that many of the competitors do not survive and die brutal deaths.
While Light Yagami was always a Villain Protagonist in the anime and manga, he started out sympathetic and well-intentioned. In the live-action films, he ends up Jumping Off the Slippery Slope much sooner than in the anime and manga, to the extent that unlike his anime/manga counterpart, he's perfectly willing to personally kill his own father to prevent the Death Note from being analyzed.
While Ryuk could hardly be considered a hero in the anime or manga, he's much more monstrous in the live-action TV drama. In the anime/manga, he just randomly dropped the Death Note and Light picked it up by chance, with Ryuk just kicking back and watching as Light carried out his plans. In the TV drama, he deliberately drops the notebook near Light and serves as The Corrupter, goading Light into killing more people when he hesitates, effectively making him responsible for Kira's existence.
L is likewise subject to this in the TV drama. Though not exactly a 'hero' (with Word of God admitting that he's a bit evil), he usually comes across as A Lighter Shade of Gray when compared to Light and a few spin-offs (namely the film L: Change the World and the light novel Another Note) portray him more sympathetically. The drama by contrast draws more attention to the amorality of his actions and he generally is far more smug and arrogant than most portrayals.
In his debut in Battle of Gods, Beerus was goofy and likable, though he did have moments of being a Jerkass God. Here, his more sympathetic qualities are toned down while his Jerkass God aspects are ramped up, doing such things as actively destroying planets after eating all their food, outright saying he never gets tired of watching planets explode after he blows them up, and going out of his way to be a dick to Vegeta and intimidate him after crashing Bulma's birthday party. Most notably, unlike in Battle of Gods where his slapping Bulma was more reflexive than anything, in Super, after Bulma slaps him, he actually turns towards her and outright backhands her across the face, all with a Slasher Smile and a glint in his eye. After the Battle of Gods adaptation, Beerus is made more in line with his film counterpart.
In the anime, Zamasu wants to murder his master Gowasu, steal Goku's body before killing him and his family, then travel to Future Trunks timeline to kill all the gods and mortals all because Goku defeated him in a sparring match. His reasons to do this is even more petty in the manga; He watched the match between Goku and Hit and becomes enraged that a mortal Saiyan like him managed to attain so much power.
Bandou was a victim of this in Elfen Lied: He was more a Jerk with a Heart of Gold in the manga. He was humanized through his relationship with Mayu and Nana. Mayu brings him food on the beach, and they are shown eating together. He saves Mayu from being raped by The Unknown Man. Then he sees Nana has been injured by one of the Unknown Man's spike balls. Since she is a Diclonius, he knows it would be troublesome for her to go to a hospital, so he treats her wound instead. He also risks his life to save Mayu from Lucy, giving up his chance for revenge against Lucy. In the anime,his part is drastically shortened, and any sympathetic or good moments were omitted, while adding in filler to make him seem more cruel.
Even Hohenheim, the Big Good in the manga, became a Retired Monster; instead of being tricked into helping Father turn the nation of Xerxes into a Philosopher's Stone, and only becoming aware of the plan once it was too late to stop it, the anime's backstory has him willingly helping Dante turn people into Philosopher's Stones to prolong their own lives.
Wrath and Envy were already horrible monsters in the manga, but the anime made them worse. Wrath (now named Pride) loses all of his Noble Demon qualities and his last scene involves him strangling his Morality Pet, his son, Envy had his sadism cranked to maximum, and both lose their Alas, Poor Villain moments.
Barry the Chopper, while Ax-Crazy in both the manga and first anime, was more of a neutral character in the former and even joins forces with Mustang before his death after realizing that he's going to be hunted down for his connection to the Fifth Lab anyway. The 2003 anime's Barry unrepentantly sides up with anyone who can help him kill as many innocent people as possible, joining up on a mission to slaughter a settlement of Ishvalans forcing Scar to step in and put him down.
Yoki in both versions starts out as a small-time villain who ends up disgraced by the Elrics, which leads him to rat out Scar to reclaim his status. There the similarities end—the manga ultimately has him becoming a reluctant and (generally) not very helpful good guy, while the anime has him killed by Lust to incite a riot between the military and the Ishbalan refugees.
In the manga, Scar's long-dead brother was an idealist whose alchemical research was motivated in large part by his desire for peace. In the 2003 anime, he became something of a Mad Scientist willing to sacrifice his own people in order to revive his dead lover, though he retained his genuine love for his brother.
An odd example comes with Anchovy, since the manga was released before the anime showed her match with Oarai. In the anime, Anchovy's competitive but fairly good-spirited, and after losing, invites the Oarai crew to eat with her and the people who set up the match. In the manga, she starts off by accusing Miho of having a "weak" way of tankery, and at the end, accuses Miho of costing her old school the championship by abandoning the flag tank.
Erika is a Jerkass in the anime, but mainly to the extent of being snide and condescending toward Miho (for example, in the finals, saying that Oarai must be weak if she became its commander). In the manga, between the semifinals and the finals, Erika flies over to Oarai, confronts Miho, and angrily accuses her of not just costing them the victory, but abandoning them in their time of crisis, and vaguely insinuates that Miho traded her vice-captaincy of her old school for captaincy of her new school. She's significantly more vicious and angry in that scene from the manga, and leaves Miho in tears at the end of it.
InuYasha: Izumo/Gyu-oh of episodes 94 and 95. The English dub of those episodes makes him a full-fledged villain, whereas the original Japanese made it clear that he was a Tragic Monster who was just driven by his madness.
In the original story, the first of the tigers unintentionally brought disaster to the jungle, but he initially wanted to kill Fear (man) to restore peace among the animals, then later out of grief for finding that all those who once looked up to him would now run away in terror. In the anime, he simply believed that killing Fear would grant him supreme power over all. The Arabic dub has the tiger attempting to frame a man for a murder he himself committed; not as aspiring a goal as the former but no less despicable.
The human owner that cared for Bagheera when he was a kitten. In the novel, Bagheera was part of a collection of exotic animals belonging to a rich rajah where he lived in luxury before escaping on his own. In the anime, the owner planned to kill Bagheera for his pelt when he grew bigger as he abused the panther along the way, the owner's daughter named Linda took care of him at that time. Later she frees Bagheera before her father can shoot him. She took the bullet, and it was unknown is she survived or not.
The Cheshire Cat in the manga adaptation of the Kingdom Hearts series is outright villainous, compared to his more neutral role in his origin book and in the game. Maleficent even offered him a place in her group, but he declined.
The Happy Mask Salesman from Majora's Mask gives the player some creepy vibes but genuinely wants to retreve the titular mask before it destroys Termina. In the manga adaptation he's heavily implied to be behind the events of the story.
Magi – Labyrinth of Magic: While Fatima is a ruthless slave trader in both the anime and the manga, both of which show him choosing to feed an Ill Girl potential slave to a pack of hyenas rather than simply give her medical treatment because it's "not worth the money," the manga also shows that he himself was once a slave who was broken down and made loyal to his mistress Umm Madaura, who, among other things, sold him as a Sex Slave to a male client. The anime completely edits out his rather horrific backstory, making him an utterly unsympathetic Jerkass.
In the Mai-HiME manga, the main antagonists of the first arc are Haruka and Yukino, the latter of whom is friends with Mai and Mikoto in the anime, and the otherwise heroic Akira assists them. By contrast, Shizuru never turns Psycho Lesbian, and Nao (reluctantly) helps the heroes after the teams merge.
Really, all of the Zeon figures except Ramba Ral are shown to be much more vile and cruel in Origin. Ramba's biological father and Char's mentor, Jimba Ral, was vaguely described as a loving father figure in the original anime. In Origin, Jimba is a borderline Conspiracy Theorist and Abusive Parent who may have shaped Char into a sociopathic Tyke Bomb. Likewise, Kycillia Zabi was originally portrayed as a stoic Chessmaster who acts out of loyalty to her family. Here, she is shown to be a violence-lovingManipulative Bitch who happily backstabs her own family members without a care in the world. Even Garma and Dolze were given more Kick the Dog moments though they are still considered the nicer Zabis.
Rather than making Garma a villain, Origin takes away his positive traits. In the anime he was shown to be a good person in general, being A Father to His Men, having a fiancée who loved him, was legitimately friends with Char (hence his shock when Char betrays him), and wants very much to prove that he deserves his command post and didn't just get promoted because his father is Zeon's leader. In Origin, he's the exact opposite of all this: a whiny Spoiled Brat who got jealous over Char's promotion, threw a literal stompy-foot temper tantrum to Daddy, got promoted (mainly because Degwin wanted him to shut up), and immediately went to Char to brag; on top of that, once he's in command he hurls wave after wave of his men into battle to earn himself glory.
Gendo Ikari: In the anime, he is Ambiguously Evil, he sincerely praises Shinji for his combat performance at one occasion, and with his Famous Last Words he regrets having been a bad father to him. In the manga adaptation, he is unquestionably evil, has a massiveGod-complex, and outright hates Shinji. In the manga, he's also implied to have personally killed Kaji, whereas it was unknown if he had anything to do with it in the anime, even though he was hinted at being involved somehow. He's somehow even worse in Neon Genesis Evangelion: Campus Apocalypse.
A few Gym Leaders aren't as nice as their game counterparts. Creepy Good Sabrina is converted into something of a demonic witch who antagonizes Ash and co., while many others, most notably Lt. Surge, Erika, and Skyla, are egotistical Jerkasses with a condescending demeanor towards their challengers (or, in Erika's case, towards those who don't appreciate the perfume her gym makes). Pryce is a Jerk with a Heart of Gold who is cold towards Pokémon due to a misunderstanding with his Piloswine long ago, although he does get better when the Piloswine is found and the situation explained. In particular, Sabrina in the games is implied to be a good-natured person who happens to have frightening powers, Pryce is a perfectly pleasant and decent man, and Lt. Surge, while cocky in the games, isn't nearly as mean about it as he is in the anime. All of them make friends with the heroes in the end. However, others, like Brock, Misty, Cilan, Iris, and Clemont, join Ash as protagonists and are more openly heroic characters.
Ocasionally used with the Pokémon themselves (particularly either Poison or Dark types). In the games and the anime itself, even Pokémon seen working for the antagonists generally aren't actually evil, just taking orders from their trainers, and aggressive wild Pokémon are only animals obeying their instincts. While genuinely evil Pokémon do exist in the anime (such as a group of Malamar in XY and an unusually mean Togepi in Diamond and Pearl), they are a minority and not representative of their species as a whole.
Giovanni was the head of a yakuza in the games but made a Heel–Face Turn after being defeated by Red and disbanded Team Rocket (though HeartGold/SoulSilver implies he intended to grow stronger and one day rebuild it). Giovanni in the anime never disbanded Team Rocket and is far more violent and cruel than his game version is portrayed.
Team Galactic is hit by this. They're a good deal more sinister and self-interested than they were in the games. Cyrus in particular becomes a lot more malevolent, with his altruistic acts and qualities removed, and his tragic backstory never brought up. Moreover, he resorts to methods far worse than anything he did in the games.
In Pokémon Black 2 and White 2, Colress, while still a scientist in the employ of Team Plasma, does encourage the player and even gives them a device needed to progress further in the game. He is involved with Team Plasma For Science! and is not particularly interested in their goals, expressing distaste for Ghetsis. After his defeat, he encourages the player to stop Ghetsis' plans. In Episode N, Colress is a true Mad Scientist who experiments on Pokémon to the point of torture, uses mind control on the Pokémon in his introductory episode (including those of the main characters), and is more than willing to hurt Ash and his friends to prove his theories. He is also more appreciative of Ghetsis due to Plasma's "providing" increasingly more difficult "subjects" pushing the theories further. Colress in the game has a Heel–Face Turn, willingly disbands Team Plasma, and becomes The Atoner after Ghetsis is defeated (which his cameo in Pokémon Sun and Moon follows through on), while his anime counterpart is arrested by Looker. The anime counterpart does come up with the idea for a Pokémon translator, but after he's arrested and in a way emphasising his Blue and Orange Morality.
Team Plasma as a whole is subject to this in Episode N. While not a pleasant group in the games, Plasma is often engaged in moral debates about their intentions under Ghetsis, sometimes questioning their motives, and eventually splitting into two factions: one genuinely concerned for Pokémon wellbeing and N's ideals, and the other being more self-centered and devoted to Ghetsis. In the anime; Plasma are outright villains with none of the moral conflicts they have in the games, fully supportive of Ghetsis' goals and posing avery large threat to Ash and his friends throughout their arc. Uniquely, this was deliberate by the writers as their initial appearance ended up being indefinitely postponed by the 2011 Tohoku earthquake and tsunami.
In Arceus and the Jewel of Life, while Marcus attempts to betray and kill Arceus using extremely heinous methods which have serious consequences in the future, he seems to genuinely believe that returning the Jewel of Life to Arceus will cause Michina Town to turn back into a wasteland and that his actions are necessary to prevent this. As it turns out, this is the case, but the inhabitants are able to restore the valley on their own. In the tie-in manga, his motivations are purely selfish — he wants to kill Arceus to become a god himself.
In Pokémon X and Y, Yveltal, despite being the Destruction Pokémon, teams up with the player to stop Team Flare's genocidal plans, just as its life-giving counterpart Xerneas does. In addition, its destruction powers are only referred to in the context of being part of its lifecycle. In Pokémon: Diancie and the Cocoon of Destruction, it is the Big Bad of the movie who seems to take joy from deliberately sucking the life out of everything around it, and is more clearly a Dark Is Evil foil to the Light Is Good Xerneas.
In the games, Mimikyu is a mischevious but Dark Is Not Evil Pokémon who imitates Pikachu because it's lonely and just wants to be loved like Pikachu. In the anime, the first Mimikyu seen is much more bitter and jealous towards Pikachu to the point of being an Evil Counterpart, even going so far as to willingly join Team Rocket. Downplayed, since other Mimikyu may have a more friendly personality.
The Spearow line in the anime are, with one or two exceptions, generally owned by villains or are malicious of their own accord, to the point of holding grudges (most famously against Ash in the first episode and the incident which led to Pidgeot's evolution). In the games, there's nothing to indicate this level of malice - while a wild Spearow flock attacks Nebby in Sun/Moon, many other Spearow and Fearow are seen living and working with people, even as affectionate house pets, with no problem, and their Pokedex entries don't portray them in a negative light compared to other bird Pokémon.
Team Flare in the XY and Z arc are more sinister and dangerous than their game iterations. In particular, Lysandre's history with Professor Sycamore and his backstory in the games as the descendant of AZ's brother and a Fallen Hero are not touched on, and in the games Xerosic eventually pulls a postgame Heel–Face Turn under the influence of Emma, a girl who befriends him. Lysandre is more than willing to lay waste to Lumiose City to accomplish his goals in the Team Flare Crisis arc; and Xerosic is not above harming Clemont for the sake of science in his appearances, with him seeking vengeance against him for stopping his plans at Prism Tower.
Some of the Gym Leaders and Elite Four members. While most of them (with the exception of Giovanni and Malva) are good guys in the games — Lance and Lorelei even helping out the player character at key points — Lt. Surge, Koga, Sabrina, Agatha, Bruno, Lorelei, Lance, Karen, Will and Pryce are villains. To be fair, though, Pryce is a more sympathetic Anti-Villain, Lance is a Well-Intentioned Extremist, and most of the other characters listed reform later on, with the exception of Agatha.
In the games, Norman is a kind, gentle person who respects his child's wishes and would most likely not use physical violence. In the manga, Norman is a lot meaner and beats up his son for disobeying him. Despite his harshness, though, he is on the side of good and is genuinely supportive of Ruby.
In Pokémon Black and White, N is a very sympathetic Anti-Villain with good intentions. He eventually makes a Heel–Face Turn in the sequel games, helping the player against Ghetsis, his much more evil adoptive father. However, N has fewer redeeming qualities here and manages to convince White's Tepig to leave her. His goal also seems to be more like Ghetsis' goal than in the games.
The manga's version of Colress is portrayed along the same lines as in the anime; being a more wicked Mad Scientist than his morally grey game counterpart.
Team Flare in the games are largely an Ineffectual Sympathetic Villain team in the vein of early Team Rocket, with the exception of Big Bad Lysandre. In the XY arc, Team Flare ends up having their more malicious elements increased and their campier ones suppressed, to the point of burning Vaniville Town to the ground in order to obtain X's Key Stone and Kanghaskhanite.
The Old Chateau ghosts and Rotom were creepy, but ultimately made little to no effort to harm the player in Pokémon Diamond and Pearl. This iteration of them, however, are much more sinister and openly terrify Cheryl.
Boy, Colress just has no luck in adaptations, huh? This version, while closer to the original in terms of motives, is still outright villainous as he is completely apathetic both to Kyurem's suffering and to the entire population of Opelucid City, whom he decides to test the dragon's power on.
Prétear: In the manga version, one of the Leafe Knights ( Sasame, the Knight of Sound) is strongly hinted to have been in love with the villain in the backstory, but he's definitively a good guy and remains that way for the entire story. In the anime, where Fenrir plays a bigger role, he eventually breaks down and becomes her minion because of his Mad Love.
Queen Beryl was a villain in the manga, but an ultimately tragic figure who was manipulated by Metaria into her crimes in her past and current incarnations, and ultimately doomed not by her villainy, but her own belief that she was beyond redemption at this point. In The '90sanime, she's a straight-up evil villain who willingly and loyally serves Metalia.
Although this is more of a case of Adaptational Anti-Heroism, Rei Hino/Sailor Mars is hit with this in the 90s anime. Rei seems more abusive towards her friends (especially to Usagi) in the anime than in the manga, especially in the first season. It's even worse in the DiC dub where Rei (or Raye as she is called in that dub) makes no qualms about wanting to kick Serena out of the Sailor Scouts and take over as the leader.
Kaede Fuyou from SHUFFLE!. While not exactly a villainess, she did, in both versions, believe that Rin was responsible for her mother's death (a misconception he encouraged to prevent her from losing the will to live), and abused him for years until learning the truth, at which point she devoted herself to him in order to atone. In the anime, in which Rin canonically goes out with their mutual friend and senpai, Asa, resulting in him spending less time with Kaede (in part not wanting her to be consumed with him), she snaps and attacks Asa, causing her to collapse, but comes to regret this later. In the visual novel, after finding out that Rin and Asa are a couple, Asa apologizes, but Kaede sadly accepts their relationship, albeit with the scene being somewhat similar to Kaede and Asa's reconciliation from the anime.
Shadow the Hedgehog in the Sonic X anime. In the games, Shadow started off a vengeful weapon ready to destroy Earth's population in honor of his murdered friend. Throughout his story however, he is portrayed with a palpable sense of doubt and emotional conflict, before ultimately pulling a full Heel–Face Turn two games later. In the anime, he roughly follows his games counterpart's story, but maintains his more sinister neutral alliance and is The Unfettered to the highest scale (at least once perfectly willing to kill a child in cold blood, along with anyone who defended her, if it meant stopping a villain).
Justin Law is an inversion: he is revealed as The Mole and is BJ's killer in the manga, whereas he stays firmly on the side of good in the anime.
In Tenchi Muyo!, Princess Ayeka is a quite haughty figure who ends up coming back down to Earth as she spends time with Tenchi and while there's a rivalry with the space pirate Ryoko, the two do have something of a friendly relationship as time goes on. While Tenchi Universe and Tenchi in Tokyo tends to ramp up these aspects, Pretty Sammy ends up turning her into an Alpha Bitch flanked by her own entourage and willing to hunt down Ryoko just because she's with Tenchi. It gets worse in Magical Project S as Ayeka is recast as a third goddess who was removed from the election to become protector of Earth and she seeks to destroy Earth because of it.
This occurs in-series in Yo-kai Watch. When Komasan reveals to a mangaka that he is really a yokai she uses him as inspiration for her manga. Sadly it is a horror manga where he is a big, scary monster instead of the cute Cartoon Creature he really is.
Youjo Senki: Tanya Degurechaff, and the HR manager she reincarnated from, become more callous and heartless with each adaptation. In the first scene alone, the light novel depicts the HR manager as doing everything to help salvage the career of the employee he would fire, but said employee is a belligerent drug addict. In the manga, he is stated to not enjoy firing his employees, but has a quota to meet to keep his company aloft, and the employee he is firing is perpetually tardy or absent and a drain on company morale due to his poor work ethic. In the anime, he is shown as selfish and only interested in advancing his own career, and thus has no qualms in firing anyone who would be an obstacle in his upward mobility in the company.
In the original Yu-Gi-Oh! manga, Rex Raptor/Dinosaur Ryuzaki, while a bit of a jerk, doesn't cheat and he did have a more helpful and honorable side. The anime's version of Rex is closer to the manga version's characterization at first, but eventually associates with more villainous characters like Dartz and Weevil Underwood in a way that Manga Rex never did, and he eventually tries to steal Joey's soul.
Bonz/Ghost Kozuka in the manga is a Punch Clock Villain working with Bandit Keith, feeling that Keith trapping Yugi, Joey and the others in a cave to get them out of the Duelist Kingdom tournament was going overboard and getting an Alas, Poor Villain death when he ends up having the misfortune to duel Yami Bakura in the Battle City tournament. In the anime Bonz has no problems with Keith trapping the others in the cave and tries to cheat by stealing everyone else's duel cards during the Battle City arc, turning him into an Asshole Victim when Bakura runs across him.
In both the original and dub version, Daitokuji-sensei is an Anti-Villain using a façade to hide his true intentions, but the façade is much, much nastier in the dub. While in the original he spends his duel with Judai giving a Not So Different speech in which he compares Judai's Fusion Monsters with the ancient practice of alchemy, in the dub he goads Judai and tells Blatant Lies about his previous victories at the Academy being the result of rigged duels. (Which he admits was untrue after losing.)
Chosaku Manjoume, or Slade Princeton in the dub has a minor case of this. In the original japanese version, after he loses to Jun (Chazz in the dub), he tells Shoji/Jagger that their little brother has grown up more than they thought and grows respect for him. None of this occurs in the dub, and he's more annoyed that he lost if anything.
The Dark World Fiends were presented as villains in the third season, which contradicts the flavor text of some of their cards in the game and the Master Guide 2, which claims they are not evil. In fact, the flavor text on Zure, Knight of Dark World's card claims that he "never oppresses the commoners", while that's probably what he's most notorious for doing in the anime.
Also, in the manga version, Jim Cook is an antagonist who is far more malicious than his lighthearted and benign anime counterpart. It's not his fault, however; he's a Brainwashed and Crazy pawn of Tragoedia.
Like Daitokuji-sensei above, Yubel also got subjected to this in the dub. While she was still a terrifying villain in the original with many horrible deeds under her belt, she was ultimately motivated by her love for Juudaiand her desire for him toremember her. The dub turned her into a straight-up psychopath who wanted to "play" with him, and because it cut out Season 4, she never had her Heel–Face Turn.
In the manga version of Yu-Gi-Oh! 5D's, pretty much every character has a different background and personality, but Rua and Ruka more so than any other. They start of as villains in this version (and rather sadistic ones at that) very unlike the kind and innocent children they are in the anime. It is later revealed that Rua underwent a Duel Dragon ceremony to save Ruka from an illness, only Luna to become enslaved by the spirit of one of the Duel Dragons and for Rua to become Brainwashed by her. Eventually, Yusei is able to use his more benevolent Dragon to break the spell.
The Synchro dimension is modeled on the situation in Yu-Gi-Oh! 5D's, but the counterparts for Neo-Domino and Satellite, the Tops and the Commons respectively, are both worse than the originals. The Tops instigated the economic inequality themselves and are proportionally a much smaller group than their original versions (they make up 1% of the population, whereas the populations of Neo-Domino and Satellite were implied to be more even). The Commons buy into the Bread and Circuses act so thoroughly they not only support the worst aspects of their world, they insult and mock Yuya for speaking out against institutionalized slavery.