Assassin's Creed III has people claim that Haytham is totally heroic and cool, ignoring that he brutally murders unarmed prisoners, tries to emotionally manipulate Conner, and plans to basically create a dictatorship with him at its head.
Organization XIII act to regain their hearts so they can become complete. People tend to forget that, in pursuit of this goal, they manipulated Sora and erased his memories, they tried to corrupt Riku, they kidnapped Kairi, they unleashed The Heartless, and they messed with many worlds. This attitude is still the same even after a game specifically about the Organization was released, with said game showing that the members of the Organization do not give a damn about each other and are complete assholes. The only one who did was Roxas, who is clearly noted to be a special case.
It has been revealed that the Organization were lied to about the state of their hearts and were pawns for Xemnas's Evil Plan. While they do start out as heartless, their hearts can be restored through connections with people, which happened to Axel, Roxas and Namine. Xemnas and Xigbar were misleading them and manipulating them to keep them from making connections so they could become vessels for Xehanort's heart. This, however, does not change the fact that they were outright antagonistic towards Sora and company and were putting lives in danger.
Axel, despite showing very few decent qualities in Chain of Memories and only helping Sora out as part of his own agenda, gained an immense following due to his looks. That, combined with his general coolness, lead to his role being tweaked in Kingdom Hearts II and the character becoming an Anti-Villain. Early trailers (like at 1:36 here and 1:12 here) shows Axel looking much more evil than he was in the finished product. He has, like Riku, undergone a genuine Heel-Face Turn in later games, but it doesn't change what he did.
Vanitas, from Kingdom Hearts: Birth by Sleep gets this treatment, despite the fact that he's sadistic and Ax-Crazy. And unlike the Organization, who do have the sympathetic backstories, Vanitas has none and is, quite literally, pure evil. He's claimed to be The Woobie being manipulated by Xehanort (he's very willfully his follower), only for the twoo wuv of Aqua (a girl he's tried to kill multiple times) to redeem him. The fact that he looks like Sora doesn't help matters.
Kane, the leader of the Brotherhood of Nod in the Command & Conquer series. It doesn't help that his motivations seem to change every game, or that the developers themselves seem infected with Evil Is Cool.
At one point in the first game, he tells the player that "people believe what the media tells them to believe... and I tell the media what to believe". Quite fitting that this is exactly what happens among the fandom - another cutscene has Kane MST the "origin of Tiberium" scene from the GDI campaign, interrupting it at one point to explain that he found it first and named it after the Roman emperor Tiberius, as opposed to Dr. Mobius finding it and naming it after the nearby Tiber River - now, look Tiberium up on Google and see how many sites mention the name's origin but conveniently forget to mention Mobius' version of the discovery (spoilers for those who don't look: the C&C Wiki is probably the only place that actually assumes Mobius to be the true discoverer).
Leon Magnus in Tales of Destiny. In the first game, he is one sadistic Jerkass who even laughs in the face of death. But fans latched into him due to his cuteness and his background, and he ends up becoming an Ensemble Dark Horse who got brought back in the sequel as Judas, who had far more good qualities and far fewer bad ones than he did pre-mortem. The developers further pandered to this fanbase in the Japan-only PS2 remake of Tales of Destiny, giving him a less antagonistic personality and making his death more honorable. Tropes Are Not Bad for his case, however, as this pandering made him more believable and liked than increasing his controversy.
Ganondorf of The Legend of Zelda series. He kills innocent people, plans hostile coups, makes people suffer, and generally passes the villain test with flying colors. However, he has his fans, due to his rugged good looks, high intelligence, and charisma, though most of them don't go as far as excusing his actions.
Given that Ocarina of Time already showed a very clear and decidedly bad outcome if Ganondorf were ever to acquire the power he's after, it just means that he's either legitimately less arrogant having already failed once before, hiding behind a more humble facade since his powers aren't restored until late in the plot or that he sincerely believes that he won't unleash a flood of evil once he acquires the complete Triforce this time.
Ghost Widow of City of Heroes generally has her fanatical loyalty to Arachnos (more of an inescapable obligation), along with the fact that she's physically bound to its existence, downplayed when discussing her, mostly because "She's so pretty...". It helps that the storyline which shows the less pleasant side of her nature requires unlocking quite early in the game, so most players don't get to see how she treats her employees.
It is revealed in one mission arc that she is incapable of not being compassionate. Her last living emotion was compassion toward Paolo, now named Wretch and however evil, however vicious she may get, she feels that compassion 24 hours a day. Indeed, the first time the player actually meets her she asks them to help Wretch because she cares about him.
There is a mission chain that requires the player to betray her. Many players refuse to even begin those missions. Some choose to turn hero instead.
Tyrant, the Praetorian counterpart to Statesman, gets some of this treatment, though thus far it is more of the Misaimed Fandom variety than quasi-romantic.
Walter Sullivan of Silent Hill 4 is most certainly screwed up beyond all reason, but his fans have an unsettlingly common habit of ignoring the nearly two dozen innocent people he brutally murdered, two of them children. It's just hard to hate a guy who's dying action is to reach for the sky and sadly ask for his mother. Part of the problem probably stems from the fact that the game portrays his child self and adult self as two separate characters. As a child, he was extremely sympathetic. He was abandoned by his parents and raised by an abusive and demonic cult. Of course, such a messed up childhood did not create a sane adult. It's likely that since the child appears regularly, a lot of people are given the impression that it still represents who he is, when it more accurately represents who he thinks he is.
Pyramid Head gets this treatment too, because he's "sexy". Even though he's a rapist and muderer. Doesn't matter, he's "sexy".
Viconia also has quite a fanboy following, many of whom try to justify her (alluded) murderous actions. It should be noted the game gives her a Freudian Excuse already, with an eventual Love Redeems option, and as a supposedly Always Chaotic Evil Drow she is much less evil than she should be.
Simply being a Death Seeker is reason enough for many fans to Woobify someone like him. Just look at Shu Shirakawa, who killed countless people, helped start at least one war, and was willing to destroy the Earth to achieve his only-a-little-bit-sympathetic goals.
Albel Nox from Star Ocean Till The End Of Time is one of the most popular characters in the game's fandom - in great part because he's incredibly hot and is voiced by Crispin Freeman (or Isshin Chiba in the Japanese version) - despite the fact that he's a sadistic jerk who tortures some NPCs for fun and insults everyone from your party members to his own king. To his credit, the game does give you the option of having him join your party permanently, which can unlock a PA that shows he's very aware of his flaws, although he's still a ruthless prick even then. His DILP status is made all the more ironic by the Double Standard many of his fans have; they like to bash MariaTraydor for being bitchy, angsty and self-centred, even though Albel is a far more bitchy and self-centred character.
Sync even has some canon points, as Van continues to use him for his Daathic Fonic Artes, despite knowing that their goals are somewhat different. Van wants to recreate the world, albeit by destroying the old one, whilst Sync seemingly wants to destroy all worlds. This may just seem like a conflict of interests, but keep in mind that Sync shows next to no true loyalty to Van, only supporting him so that at least the old world will be destroyed. For a man whose goals will destroy the world out of necessity rather than an explicit desire, he's certainly doesn't seem to care that his left-hand man isn't at all compassionate.
Albedo from the Xenosaga series has a good amount of fans who claim that he's "just misunderstood", despite the fact that he put Cute Realian Girl MOMO through horrible Mind Rape, tortures his twin brother Jr. with mind tricks and taunts, destroyed an entire Federation battalion with Proto Merkavah for a warmup, his merging with a space-time anomaly that he would put to use by wiping out the world, and the fact that he's a psychopath who's a Nietzsche Wannabe with A God Am I complex. This results in him getting paired with MOMO (albeit sometimes an older version, but sometimes not), Gaignun Kukai (a.k.a "Nigredo"), and even Jr. himself.
Specter from Ape Escape. The fact that he is a monkey may have something to do with it.
This is done in Tsukihime fandom to Nrvnsqr Chaos and Roa. True, they are complex villains with personalities who go much beyond the cookie-cutter bad person (and actually get sympathetic on occasion in Roa's case), but the writer seemed to have forgotten that, in the end, they were still villains.
Nu-13 as well. If anything's blatant, she hates everything else except Ragna, and her preferred method is 'stab everything on her path in a jealous rage, even if the world goes boom'. She's a Weapon of Mass Destruction only hell bent to get laid with Ragna and no one else shall have him. Fan reaction? Because she executes such 'love' with such adorable (if creepy) love and cute look as well as some crazy representation like 'Pirate/Valley Girl Nu', everyone thinks she's just a pitiful, lonely soul who longs Ragna's love. Never mind that she hates the world and only wants Ragna for herself.
Kokonoe is a Villain Protagonist version. Because of her physical attractiveness, snarkiness, being the offspring of two Six Heroes Jubei and Nine, and the fact her main opposition is the vile Hazama/Terumi, many of her atrocities including her treatment of Lambda, helping Relius Clover create Ignis, and having nukes trained on Kagutsuchi ready to fire as a plan B if her revenge gambit backfires, are glossed over. Since this goal was so 'important', she also usually gets excused for not helping Litchi save Arakune despite her soft spot on Litchi (and her being Forced Into Evil is treated like it's never Kokonoe's fault), and going every way to ensure Bullet will never get the information she wants or get near Tager (and even gave Tager the order to kill Bullet for whatever reason). The story seems to pander it up to as up until Chronophantasma, although she received several calling outs, the storytailoredit that no one becomes sickened enough of her to boot her from the team lest she removes the 'Villain' part on the Villain Protagonist on her and no other 'great genius with better morals' popped up so Kokonoe will always be protagonistic and always treated as a Face.
Vamp. Fan Fic writers tend to treat him as this utterly tragic figure who just wants to be loved, all the while conveniently forgetting that he's a terrorist and a blood-drinking murderer who killed an innocent, defenseless girl for no discernible reason. This treatment seems to be from the effect of his looks.
Colonel Volgin, a mass murderer, gets a surprising amount of leeway from many fans purely because of his Morality Pet lover Raikov.
Big Boss himself, although his is a special case. His backstory in Metal Gear Solid 3: Snake Eater painted him as a genuinely sympathetic character, causing fans to go so far as to excuse, if not outright defend his less than admirable actions in Metal Gear and Metal Gear 2: Solid Snake. Some have even gone so far as to call Big Boss the true hero of the series for his intention to rebel against the Patriots' control, never mind Big Boss himself calling his son, Solid Snake, a better man than he ever would be.
World of Warcraft has, The Lich King (more specifically Arthas), Illidan Stormrage, and Kael'thas Sunstrider. To be fair, all three of them have very sympathetic backstories, Arthas had his soul cut out and still shows signs of being a Benevolent Boss sometimes.
Both Kael'thas and Illidan have similar issues, thanks toRetCons that have essentially split both of them, particularly Kael'thas, into two completely separate characters: one pre-Burning Crusade good guy (or at least anti-hero) and one post-Burning Crusade straight up villain. That fact has even led to Blizzard vowing to bring Illidan back with a redemption story, while regretting that they already wasted their chance with Kael'thas' resurrection.
Sylvanas as well, as players tend to sympathize with her tragic backstory (her homeland gets destroyed by the Scourge, she gets killed and raised as an undead), and tend to view her as the leader and protector of a race of undead outcasts. Unfortunately, she was responsible for ordering the creation of the New Plague, (even if Putress used it at the Wrathgate and was working for Varimathras, she's still using it in Cataclysm), betrayed and killed the humans whom she promised to help retake Lordaeron (who admittedly were led by a racistAsshole Victim), and even raising the undead to give the Forsaken the manpower it needs to fight the Alliance. It doesn't help that she's one of the most beautiful female characters, even after her death, and many fans even argued that she didn't order the creation of the new plague and didn't even know it was being produced. (The theory goes that all the questgivers were either lying or misinformed when they said they were making the plague for Sylvanas. Many other fans of her character would rather have her evil than this incompetent.)
Horde players will often cite her as one of their favorite or at least best leaders, despite the fact that neither Thrall nor Garrosh trust her, and she has earned that distrust by disobeying orders about not using horrific biological weapons against a kingdom that was not only neutral at the time (her actions drove them into the Alliance), but was completely isolationist and not bothering anyone. Vocal Forsaken players in particular love to say that anything they do is not for the Horde, but "For the Dark Lady," even after the following point was revealed.
Garrosh Hellscream got a lot of this early on, when he appeared more sympathetic, though even after he's been firmly established as a villain, you can still find people claiming he's the best Warchief the Horde has had. Initially, Garrosh was a depressed man ashamed of his father's villainy. Thrall explained to him that his father redeemed himself and he became a major player in the Horde. It didn't take long, however, for him to be revealed to be a brash, violent person, and that recklessness even stopped the Alliance and Horde from working to contain an Eldritch Abomination (leaving the players to handle it themselves). While there were times when it seemed that his sense of honor prevented him from being truly evil, he seemed to believe that killing children was okay if you had a reason to believe they'd become your enemies in the future, and Mists of Pandaria finally revealed that his orcish sense of honor is deeply tied into his sense of orcish superiority. There are still plenty of non-orc Horde players that insist he's a hero to the Horde who just wants his citizens to have a good life with lots of land and resources, despite the fact that he is now a genocidal tyrant who wants to murder every living thing that is not an orc absolutely devoted to him. At least one short story shows a vision from a possible future that shows that if he got his way, the world would ultimately be destroyed because there would be no one but him and some orcs to stand up against all the other evils in the universe.
It didn't help as Cataclysm presented him as sympathetic or badass most of the time and that a lot of game developers actually defended his views, and even continue to do so in Mists of Pandaria, so it's very likely that Metzen himself was either dissatisfied with the character or caved in to complaints from Thrall fans and did so on their behalf.
Maiev Shadowsong at least gets a misinformed version of this, due to most World of Warcraft fans never having played Warcraft III, and having their first exposure to her being in the final fight against Illidan, where she's your ally. In Warcraft III's expansion, she was introduced as Illidan's Inspector Javert. She was responsible for keeping watch over Illidan, and did not care that it was her own queen who released him in order to help save the world. She massacred anyone who stood in her way on her search for Illidan, and expressed disgust toward her sister race, the Naga. Eventually, she risked the life of her own queen and religious leader by lying to Malfurion about Illidan. Fortunately, Kael'thas was able to reveal that Tyrande was probably still alive, and gave Furion and Illidan time to save her. Afterward, Maiev chased Illidan to another planet that her leaders had banished him to, and was ultimately thought to have died. Then when she reappears again in the Wolfheart novel, she searches for purpose, and ultimately turns against her own people for accepting the Highborne, Worgen, and other Alliance races into their fold. She goes on to decide that only she knows what justice is, and frames others for murder as part of a plot to assassinate many of her own people. Ultimately, most of her allies are killed and she is chased off once more. Many World of Warcraft fans called this a betrayal of her character, since they never saw how she was originally, and have been characterizing her themselves as the only sane one in a world of collaborators.
The Scarlet Crusade is a bunch of insane Knights Templar and Crazy Survivalists who have been shown killing on sight anybody who wasn't human (and even then this generally isn'tenough), burning down villages just in case they might carry the undeath plague, and routinely torturing and executing innocent civilians. But since they are enemies of the Forsaken mentioned above (among, again, everybody else), and one of their leaders is a white-haired woman with a thong-revealing outfit, this hasn't stopped many fans to argue that they never did anything wrong and are actually noble people who should join the Alliance to fight the despicable Forsaken. The same Alliance which, by the way, also wants the Crusaders dead for killing its citizens on sight.
Many Alliance fanboys try to excuse Daelin Proudmoore's actions, claiming that he was right about the horde being evil and that Jaina should have just killed them all. They ignore that Daelin's actions played a massive role in making Orcs hate the alliance, meaning that if anything the events of Garrosh's rise are at least partially DAELIN'S fault.
William Birkin from the Resident Evil series. Never mind the fact that he (and Albert Wesker) killed a fellow scientist just so he could take over his research, never mind that he conducted inhumane experiments on human test subjects and was responsible for the creation of several monsters (he was the one who created the Hunters), never mind the fact that he injected himself with his own creation (the G-Virus) and tries to mutate his own daughter into another G-Mutant (granted only after he turned into a mindless monster).... all the fans really care about is that he's a Tragic Monster. It doesn't hurt that he was a loving husband and father as well.
Wesker himself. This is a man who has betrayed and tried to kill the main characters, subjected innocent civilians to an experimental zombie outbreak, abducted and brainwashed Jill Valentine, and tried to wipe out the majority of life on Earth via bio-terrorism so he can play God. But due to his intelligence and voice actor, there are fans who legitimately think he should get to take over the world. It was lampshaded in Resident Evil 5 with Excella, who fetishized every screwed-up thing he did and acted like they were destined to be together. Not only does Wesker not care about her advances, but he turns her into a monster to slow down the good guys.
Vile from Mega Man X. Fans like to pair him with X, forgetting that he loathes X in canon and tried to kill him. Repeatedly. Later though, Maverick Hunter X made Vile a playable character and changed the story to accomodate him as a Nominal Hero instead of completely evil (though he still hates X).
Dynamo, who admittedly has a cool design, a double-sided beam saber and awesome boss music. Too bad fans forget that he tried to drop a colony on the planet, was creepily subservient to Sigma, tried to stop the heroes from saving the planet, and had a cheerily fun time doing it. Yet people like to write him as a lovable goofy prankster who joins the Hunters.
Pick any Spyro the Dragon villain, any at all. It's really severe with Ripto, Red, and Malefor.
ZEX from Star Control 2 is not exactly a nice guy (he does try to add the Captain to his menagerie, and all), but a startlingly large portion of the fandom sees him as a poor, misunderstood, mistreated woobie who just wants to live happily ever after getting it on with the Captain.
The Eldritch Abomination Zero of the Kirby series has some fans rationalising that it wants to spread misery as a result of jealousy towards those who experience positive emotions. Or rather that it's just lonely and wants friends, despite nothing indicating such a thing.
Speaking of Kirby, two other villians who constantly get this treatment are Marx from Kirby Super Star and Magolor from Kirby's Return to Dream Land. Many fans ignore or refuse to accept the fact that these two are Manipulative Bastards that tricked Kirby into helping them take over Pop Star (Marx) and the entire universe (Magolor). A lot of fanart for these two portray them as cute innocent guys who mean no harm instead of being evil. It doesn't help that both of them do look pretty cute.
Saren Arterius of Mass Effect is occasionally a subject of this. While the ending has him being convinced by Shepard that he screwed up on trying to contain the Reapers and only made everything worse because he fell to their indoctrination, and it is even possible to get him to shoot himself in the head and end his cooperation with Sovereign, this does in no way negate the fact that he was a very horrible person with thousands of bystanders as casualties when on missions for the Council, only to prove his racist points.
In the second game, he's evidently considered this in-universe as the Shadow Broker DLC reveals that there exists a documentary entitled Saren: A Hero Betrayed. Watching this (amongst other things) apparently drove Captain Anderson into drinking.
Cerberus and its leader, the Illusive Man, are initially the only ones who believe Shepard about the Reapers and provide him with an enormous amount to tools to aid in the fight against them, including literally bringing him back from the dead. Indeed, the galaxy would have been screwed without them. They're also a human supremacistterrorist organization that want to secure human dominance in the galaxy by any means necessary, including experimenting on children, attacking the Quarian flotilla, and collecting Reaper technology. Inevitably, there are some who ignore the latter in favor of focusing on the former.
In fact, this is deliberately invoked in-game. As Shepard will learn in the subsequent game that the Illusive Man made sure Shepard's crew consisted of the people who knew the least about Cerberus' true agenda and who's attitudes were most in line with Shepard's which makes player sympathy for Cerberus almost inevitable.
Kai Leng, a xenophobic who tortured and killed various aliens (and a human) in horrific ways. It helps that he looks like a cross between Raiden and a Final Fantasy character.
Bizarrely enough, the Reapers themselves. Some particularly sociopathic fans attempt to justify their unfathomable acts of repeated mass genocide, Mind Rape and torture through the Reaper's own insane and easily disprovable reasoning for their actions, even arguing that allowing the galaxy to fall under their rule or supervision is somehow a good thing.
Mass Effect 2 introduces Secret Character Morinth, who is an Asari "Ardat Yakshi", or "vampiricspace succubus" whose own mother describes her as a monster. She's a sociopath who is quite literally addicted to killing people by overloading their nervous systems during her Mind Link Sex, favors preying on the emotionally weak and vulnerable, and will gladly sacrifice entire villages to cover her tracks. Despite this, she gets a lot of supporters who defend her actions because "she didn't ask to be born an Ardat Yakshi" (she inherited the genes from her mother as a result of her mating with other Asari) and because of the rather draconian measures Asari take to keep Ardat Yakshi under control (enforced chastity and imprisonment in a monastery-colony for the rest of her life, or execution). Her own mother sadly praising her as the "brightest and best of my daughters" only fuels the flames.
Dragon Age has three big ones:
Loghain mac Tir of Dragon Age: Origins is starting to get the Leather Pants, though it seems largely confined to Alistair's hatedom (yes, even he has one, though it's small). Loghain's literal Pet the Dog moments if you recruit him to the Grey Wardens and backstory in the prequel novels seem to encourage it. But even aside from that, a lot of fans like to insist that he is actually the true hero of the story. This usually involves blaming other characters for his mistakes and misdeeds, such as when he abandoned the king and half the army to die at Ostagar, they say that Loghain's victims were either secretly evil, and therefor Loghain was right to try and get rid of them, or that they were morons, and Loghain had no choice when he left everyone to die. A lot of the actions that can't really be justified (selling citizens as slaves, torturing dissenters, slaughtering entire families) get blamed on Arl Howe, who is somehow the only one responsible for these things despite the fact that he is working for Loghain. It doesn't help that Wordof God confirmed that Cailan's plan was to ditch Anora after Ostagar in favor of the Empress of Orlais, which would have united the two rival nations. This makes Loghain's paranoia less insane. Also, in the book The Calling, it was shown that his distrust for Grey Wardens has an actual basis because from his point of view, they kidnapped Maric and almost got him killed. Word of God also added some retroactive whitewashing, i.e. claiming that while he did arrange for the poisoning of Arl Eamon, he didn't mean to poison him to death (though the poisoning was apparently so effective that it could only be cured by a miraculous relic).
Also, the fact that Loghain ultimately takes his impending execution (if you so choose) with quiet dignity, actually asking Anora to stop protesting it whereas Alistair throws a hissy fit and storms off forever if you don't do what he wants earns him many points among fans.
Some even try to justify selling the city elves to Tevinter (which he acknowledges doing at the Landsmeet if confronted, while he has no problem blaming other things on Howe). Apparently the fact that they're third-class citizens who can be assaulted and murdered with impunity means it doesn't matter that he takes it another step.
Anders in Dragon Age II became possessed by a spirit of justice/vengeance, and blows up a chantry, but some extreme fans excuse and absolve his actions. The fact that he is a love interest for a male or female protagonist in the second game doesn't help matters either - it is popular to pair Nathaniel Howe and Fenris (who hates him) with Anders for some reason. These fans apparently forget that Anders' method of dealing with a problem is to run away or destroy it, and also that Anders being bisexual and a mage doesn't absolve his crimes. The general Grey and Gray Morality doesn't really help, nor does the fact that, well, he's being possessed. That being said, just like with Loghain, there are those who fit him for leather pants, and then there are those who ignore all of his points and just paint him as irredeemable.
Ser Cullen (from both Dragon Age games) gets nearly as much of this. Having an awkward crush on a mage he's expected to kill should she get "out of line" is apparently romantic (to give the man some credit, he knows better than to act on it). Then Uldred tortures and kills most of his friends, leaving him champing at the bit to wipe out the Circle altogether. In one ending, when a mage Warden asks the reigning monarch to free the Ferelden Circle, Cullen snaps and murders several apprentices. In the sequel, being one of the few Templars in Kirkwall you can reason with at all encourages people to think of him as "moderate", despite the fact that he openly says mages are weapons rather than people. He spends years as Meredith's right hand in the most abusive Circle in Thedas, either ignoring or tacitly condoning the actions of people like Ser Alrik. Six years later, if you encourage him to kill Alain, who's been sexually abused by Cullen's fellow Templars, Cullen doesn't bat an eyelid. He only decides to oppose Meredith at the absolute last minute, after she's already tried to murder the Circle for the crime Anders (an apostate) committed.
A Dance with Rogues has Vico, a violent and cruel Blackguard who works for the game's criminal organization that the Princess is forced to be a part of. Although he saves the Princess' life at the beginning of the game, he also callously informs her of her family's gruesome fate, after which he rapes her as revenge for what her father did, constantly mocks her later, makes snide comments towards her, including Slut Shaming her, and so on. In Part Two upon asking him why he raped her, Vico will blame her for it. Throughout the game it's also shown that he's incapable of normal communication, hates people for any perceived weakness and inability to protect themselves and loves fighting, killing and sex and will enjoy doing so every time he's allowed. For some reason he's apparently the most popular of the romance options. And while true that Vico has some good qualities and a Freudian Excuse past, he only reveals that if the Princess accepts his advances and will only then apologize for raping her, and only if she asks him about it. If rejected as a lover, even if still on friendly terms, he opts instead to turn on her, and even if romanced, at one point he shows he's willing to sacrifice the Princess if it means saving his own life. Choosing him as a lover also doesn't make any exceptional change in him. But because he treats her better when romanced, is apparently good at sex and even comes around to accepting that the Princess carries his baby and refuses to abandon her even so (being a well known former casanova that refused commitment and all), apparently a lot of players are willing to overlook everything else.
Some players of Shadow Hearts: From the New World claim that the villains are the most sympathetic people in the game. Said villains are Lady, a soulless mass of evil trying to destroy the world and killing almost anyone standing in her way, and Killer, a serial killer with no motivation beyond sadism and loyalty to Lady.
Tohru Adachi of Persona 4. Keep in mind that he threatened Nanako to get to the main characters, and arranged for her appearance on the Midnight Channel so Namatame would abduct her, which would have killed her if they didn't catch him in time. Many fans like to take the fact that he seems to turn around in the end as a sign that he's not as evil as he seems.
As well as Mitsuo Kubo who's nihilism fits well with some of the people who think he is much cooler since he rejected his shadow completely.
And then there are the people who feel sorry for him because they find him so pathetic. The drastic lengths he goes to just for attention, his Shadow, and the extreme ostracization he's implied to have gone through make him a Jerkass Woobie taken to the extreme.
Lucifer in the Shin Megami Tensei series. People forget that he's the premier Fallen Angel, a Magnificent and Manipulative Bastard, whose goals, when viewed logically, wouldn't look out of place in Warhammer 40,000 - the ultimate destruction of all worldly law and order, the release of all the madness and chaos of the human heart. He's literally Chaos incarnate - and while he honestly wants Humanity to survive, it's because the human spirit is the key to everything in the SMT'verse. He's vicious and ruthless, calmly planning a Z-Class Apocalypse Howone day, popping up for a test match the next, tampering with established history tomorrow and playing with some humans for fun some other day.
Though as of more recent games, Lucifer really isn't any better. He's just far better at hiding his intentions, making YHVH the far more overt evil.
Colonel Autumn of Fallout 3 has legions of fans. Nevermind that he's part of a racist, genocidal fascist group. Nevermind that he murders an innocent woman in cold blood and drives the player character's father to Heroic Sacrifice. Nevermind that even at the end, the only difference between his and Eden's plan is that he doesn't plan to commit genocide, but still intends to use his control over Project Purity to turn the Wasteland into an oppresive, iron-fisted fascist dystopia...
The Enclave in general gets this treatment with a fanbase trying to spin them into having some sort of noble intentions. The Enclave were a shadow government organization that instigated a nuclear war they assumed only they would be prepared for to wipe everyone out. They are anti-mutant, but their definition of "mutant" is anyone that isn't pure bred Enclave. Their ultimate goal is mass genocide and their largest detractors tend to be former members of the Enclave.
Mr. Burke, due in large part to having exactly the same voice as Lucien Lachance from Oblivion. It's no coincidence that a lot of female PCs take the Black Widow perk around the same time they enter Megaton.
Caesar. According to many players he's simply a perfectly lovely fellow who's only using the Legion's brutality to bring order to the Wasteland. This convientantly misses the slight quibble of him wiping out an entire city and attempting to extermiante a further two tribes simply to spite Joshua Graham. Or his blunt admission that he enjoys murdering his enemies. Or his scolding the Courier for not enjoying violence for the Hell of it if you try to save Benny. Or him threatening to torture you to death for his enjoyment if you quit the Legion. Or making thinly veiled death threats if you ask about his defeat at Hoover Dam. And then there is the whole issue of him running a giant empire where slavery, human sacrifice, sadism and the extermination of the elderly, ill and homosexuals are accepted practises.
In a few cases, many players felt this effect about themselves after they acted in a way that they felt was right, but didn't gel with what Word of God held to be. A notable case is Roy, a ghoul victimized by prejudice in Tenpenny Tower and wanting revenge. The policy certainly comes off as unjust, and indeed, the ruler of Tenpenny Tower is very evil and killing him is treated as good. Roy's revenge scheme, however, is letting legimitely-insane ghouls in to slaughter all of the occupants, including one who once had a beloved heroic ghoul as a friend. Yet the game treats killing him as evil, and most players unsurprisingly disagree. Similarly, the game heaps scorn on players for going against Ashur in The Pitt and Mr. House in New Vegas, despite the fact that the game never gave any hint that they had sympathetic sides until after the fact.
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 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 gets this a good bit too, mostly since he's easily the biggest asshole of the rivals in the series (what with Blue basically just being kind of a brat, and the others all being friendly). Between stealing from Elm, kicking you in what is one of the only direct act of violence from a human in the series, stripping you, and having a stock pretty boy look (albeit with red hair), he's such a Badass that people tend to love him. Helps that he does get a Heel-Face Turn, and is Giovanni's son.
Giovanni himself gets this too, due to him being a rather handsome Yakuza/Mafia crime boss with nice clothes to boot.
Ghetsis has neither a sympathetic backstory nor redeeming qualities nor outstanding beauty, so it must be his sheer bastardy charisma that earns him so many fangirls.
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 is probably why Pokémon Special decided to make him muchlesssympathetic.
Quite a few of the villains in Mortal Kombat (especially Mileena, Shang Tsung, and Sektor) have quite a few more fans than you'd expect.
The characters from Team Fortress 2 got this even before they showed any good tendencies (particularly The Medic and the Spy) their psychoses and enjoyment of murder being utterly removed in favor of depictions by fanfic authors as Shell-Shocked Veterans.
The Origami Killer (a.k.a. Scott Shelby) in Heavy Rain Not only is he the most Badassplayer character in the game, he also has numerous Pet the Dog moments long, long before The Reveal. This is compounded when you see how crappy his childhood was, and that he's doing all this to get back at fathers that don't love their kids. The problem? He's murdering children. By the time the game starts, he's already killed at least eight people, not counting the parents that vanished trying to save their sons. Even if you find Shaun, he'll gladly shoot you in the back and let your son drown.
Kratos of God of War, who's Badassery in enough that fans make excuses for his more evil actions. (Some people say that his actions were somewhat justified because the Greek gods messed with his life; of course, a list of people who's lives were ruined in actualGreek Mythology because the Greek gods "messed with their lives" (compared to, say, Heracles, Kratos was lucky) would fill a very large book, and lots of them turned out to be far more benign than he was.)
The infected in Left 4 Dead. There is a disturbing amount of shipping works starring them, and the Witch is often branded The Woobie, because she's always crying. The Hunter, on the other hand, is often depicted as an attractive young man beneath his hood despite how decayed his face looks in the actual game.
Vivec of The Elder Scrolls III: Morrowind is an interesting case. A man who, along with Almalexia and Sotha Sil, betrayed and murdered Nerevar, used ancient technology to become a living god and illegally ruled over Morrowind, presiding over a regime rife with slavery and inequity.
Almalexia and the entire Tribunal often get this treatment: Almalexia because she's sexy, the Tribunal as a whole because of its Crazy Awesome holy books.
While we don't know much about Sotha Sil, Almalexia seems to be the only one from the Tribunal that can really be considered unambiguously "villainous" (at least during the time of the game). Vivec is no paragon of virtue, but unlike most examples of this trope, he's more grey than black, and a case can be made in his favor. He's done good for Morrowind and its people over the millennia, and he does protect his people...as long as they worship and love him.
Lucien Lachance in Oblivion. Evil? Yes. Creepy stalker? Certainly. The Dragon to a death-cult of assassins who kill people mostly just to appease a cosmic entity that probably doesn't even care? Obviously. Perhaps the greatest Mr. Fanservice in the game? Oh yes. And it doesn't stop at the fans — since the Dark Brotherhood, to whom Lachance belongs, is a joinable faction for a Villain Protagonist character, his status as the player's mentor makes him widely praised even though he is an acknowledged avid supporter of all the atrocities commited by the Dark Brotherhood and encourages the player to carry these out.
Lucien is popular enough that in Skyrimhe's back as a summonable spirit.
Speaking of Oblivion, we have the Blackwood Company, the rival guild of mercenaries to the Fighters' Guild and the main antagonists to the Fighters' Guild questline. They appear as merely slightly more unscrupulous, edgier mercenaries than the Guild for much of the questline, until you're asked to infiltrate and discover that the Blackwood Company keep a tree known for its hallucinogenic sap in the basement of their headquarters, bottle the sap, and give it out to new members during the initiation ceremony, making them hallucinate monsters and unknowingly slaughter innocent civilians. Which you get to experience firsthand. But does this do anything to stop the fans from wishing they could join the Company for real? No. Maybe it's because of the uniforms.
For the most part, the Thalmor of Skyrim came off exactly the way the devs intended. One commentator noted that most people hate the Nazi elves more than they hate Alduin, the dragon-god trying to eat the world. And yet some fans inexplicably like them. Maybe it's the uniforms again, or maybe they're just being contrary. Surely they don't support religious persecution, genocide and purges, or forcing a treaty at the point of a sword.
Then you have those people who wish they could Take a Third Option and join the Forsworn, the Breton natives of the Reach who have been driven off their land by the Nords, who use them for slave labour, and seek to reclaim it for themselves as an independent kingdom. Oh, and they also plan to commit genocide against the Nords if they do get their way, and the game heavily implies that the bulk of their fighting force is made up of Psychos For Hire who eat their victims and wear their skin as clothing. No points for guessing what part of that description most people tend to bring up, and what part they don't.
Alva, the vampire lady in Morthal. Put that one down to Evil Is Sexy.
Also in Skyrim, Cicero. A creepy, babbling madman wearing a jester costume in the employ of the Dark Brotherhood Assassins. He's an Ax-Crazy murderer for hire, who giggles and sings about killing people, admires a serial killer, and mutters frequently about oiling the Night Mother in "all the hard to reach places". Yet many fanfics turn him into a misunderstood Broken Bird with many sympathetic qualities and ramped up sexiness and sensuality, often paired romantically with a Dark Brotherhood aligned Dragonborn.
Aran Ryan in Punch-Out Wii. Just take a look in deviantART and see him turn from "Complete Lunatic" into "Irish Hottie".
Godot from Ace Attorney. Granted, he's much more sympathetic than many of the villains in the series, and the murder he committed was out of defense of another, but the fact remains that the murder could have easily been avoided - he deliberately allowed the situation to reach the point where he had to kill, and yet most fans don't even treat him like a villain. It's probably because the writers themselves kept trying to play down his faults.
In the fourth game, Valant counts too. Zak may be the bigger jerk overall, but trying to frame him is still a bad thing. Not that many of the fans want to believe that. (At least he shows contrition for what he did though)
In the first game, at least, you could also place Miles Edgeworth into this catagory, as he is portrayed as the antagonist for much of the first game, being an Amoral Attorney who primarily cares about winning. This is credited to his really sad back-story Namely; the DL-6 incident, and that he thought he'd killed his father for fifteen years. and a fair amount of Depending on the Writer involved; some cases have him using underhanded tactics to secure a guilty verdict (1-2, 3-4), while Case 1-5 suggests that he never intentionally forged evidence, which makes it easier to gloss over his earlier tactics and motivation.
Fans often make out Manousuke Naito in Investigations 2 to be far more sympathetic than he actually is. Sure, he does have a tragic backstory and a close friendship with another character, but people seem to forget that he murdered a fellow bodyguard in cold blood out of sheer jealousy, and shows absolutley no remorse over it. In fact, he goes so far as to harshly insult him after his death, in front of his boss! That and during Case 1 he takes a level in Jerkass so extreme he makes even Daryan look tame. Admitedly though, all the killers in this game (with the exception of Bansai Ichiyanagi) have at least some sympathetic qualities, so they're just asking for this treatment.
It doesn't hurt that Squall is at least as much of an immature jackass for much if not all of the game depending on who you ask, moreover the story implies Seifer was under mind control for at least his more objectionable actions, and the ending shows us he gets better.
Bowser was heightened to this status by some, after Paper Mario confirmed that he's had a crush on Peach since the series began. What seems to be conveniently overlooked in these fantasies, however, is that he's an uncompromising brute who is seemingly incapable of expressing any feelings softer than "I get what I want or I punch your nose in," which is all part of his charm, of course. Still, in some of the latest games, he has unwittingly proved to be even slightly capable of some goodness, which is a bit contradictory for an Evil Overlord, Big Bad, or Card-Carrying Villain. The uncompromising brute he usually is is currently more of a selfish, immature Jerkass than pure villain and might not get him what he wants anymore, just likely piss off everybody.
A far, far worse offender is Dimentio. Unlike Bowser, he has absolutelynoredeemingfeatures and is probably the single most evil character in all of Mario history. This completely goes over the heads of his fangirls, who insist on portraying him in a sympathetic light or just outright forgetting that he's supposed to be a villain.
While Kain of Legacy of Kain] isn't without sympathetic qualities and somewhat noble motivations, he is still a vicious Evil Overlord who will kill anyone who gets in his way and laughs in amusement as he drinks the blood from helpless prisoners chained to walls who beg him for help. Many fans, both those trying to justify his evil because he's such a badass and those trying to justify their Perverse Sexual Lust for him, try to gloss over his less heroic aspects and focus on the fact he's trying to save the world, ignoring the fact that he's trying to save the world so he can rule it and enslave humanity. Of course, there is a large section of the fanbase that not only acknowledges the evil side of the character, but love him for it. He also strides around in a pair of actual leather pants.
Many fans think the title character of Shadow the Hedgehog just needs a sympathetic hug. Okay, he's not a villain as such now, but he's still ruthless, arrogant and chilly.
Since Anti-Sonic became Scourge in the Archie Comics, he's been getting more of it. Fans are now hitching onto the shades and leather jacket and saying all he needs is a bit of love, despite the comic not even trying to hide the fact that he's a remorseless womaniser who once tried to beat an unconscious old echidna to death with a rock. He'll take your lovin', and that of every other girl in the line. And he's got even less chance of changing than Shadow, thanks to having arrogance that is cranked Up to Eleven.
This trope is very apparent with Sonic the Comic fans. Super Sonic is the most popular character outside of the more hardcore fandom, despite it repeatedly being shown he's a sadistic, sociopathic, and arrogant Omnicidal Maniac. Admittedly the comic shows he's not so bad when he loses his memory or stops using his powers - in fact he's a bit of a loser. But it seems that his default action upon using his powers in any way is to try and destroy the planet with them.
While Tekken's Nina Williams isn't explicitly a villain, she'sdescribed in-game as a cold-blooded, heartless assassin. She has no problems attempting to assassinate her son, and her depiction in the games is at best, as an amoral mercenary. But because she's a gorgeous blonde and the most badass of the female characters, she's become such an ensemble darkhorse that she even got her own spinoff game.
Kazuya Mishima is another example. After apparently being Killed Off for Real, he amassed popularity enough to return. And he is still a massive bastard after resurrection, or even more. Still, he's a badass at doing his job and at least has a bad enough past and a soft spot of sorts on Jun Kazama, so there are some who justifies in making him less monstrous than he is in the game. Granted, Heihachi is more or less responsible for the utter mess that he is right now. On the other hand, Heihachi himself also gets his pass for his utter Badass Normal credentials, more visible Pet the Dog with Kuma (his pet bear) and the fact that Kazuya's practice as the head of Zaibatsu is just utterly brutal and open while Heihachi's more benevolent... never mind that in the end, those benevolent acts are just masks to cover Heihachi's own nefarious plans. So right now, Kazuya and Heihachi are competing on whose leather pants are shinier.
Fable II and III: Oh, Reaver. You kill people who speak against you, destroyed all of Oakvale, you're a complete Jerkass, and you have no morals. At all. So why, why do the fans paint you as a broken, tragic soul whose sociopathic, self-centered behavior is only a mask to hide the poor, sweet soul underneath? Why is your entire personality ignored? Could it have something to do with being voiced by Stephen Fry?
The Star Wolf mercenary group in Star Fox. Leader Wolf, while honorable, is a self-centered jerkass who pined at least nine to eleven years (spanning the time frame of the series) for revenge against one guy, and tried to kill him and his group for an unclear reason beforehand; Leon is supposedly an Ax-Crazy killer, and though Panther is The Dandy and the least aggressive of the group, he still commits crimes and will kill anyone when he must. Expect all three, especially Wolf, to be painted as woobifiedBroken Birds who had the most brutal of backgrounds and are really innocent souls on the inside. Also expect them to find solace in a romance with another male member of the cast.
Maximilian, despite being an aloof, calculating bastard who treats Selvaria like garbage which she accepts due to her unrequited love. The fact that he's an unrepentant jerk is brushed off by his supporters, pointing to the fact that he "rescued" Selvaria from Imperial experimentation (ignoring that he himself uses her as a disposable weapon) and that he (apparently) objects to war crimes and punishes those who commit them (while committing several himself).
Jaeger, because he's rugged and cool and has a big cool tank and he's fighting for his nation's freedom! Nevermind the fact that to achieve that freedom he's willing to sell any other nation he can down the river to the empire while being a smug idiot who thinks only his problems matter.
Kuja from Final Fantasy IX is a smug bastard that manipulates people to gain power, kills the princess' mother, taunts Vivi on how he was manufactured instead of being a real person, and throws a cosmic tantrum when he finds out that his life span is short, so he destroys a planet and seeks to end all forms of life as a response. Many fans view Kuja as a poor sympathetic guy who is brainwashed to destroy and just needs some affection. While he gets an Alas, Poor Villain death, this assessment is inaccurate.
Jirall, from The Last Story, is actually a deconstruction of the concept. He thinks he's a Draco but is Wrong Genre Savvy to the max. As a result, nobody takes him seriously and he becomes increasingly desperate and insane in his bids for power and respect... all the while never considering that the first solution to getting them might be to stop acting like such a douche.
Lezard Valeth of Valkyrie Profile. In the game itself, he's depicted as a creepy stalker, callous to everyone, needlessly cruel and murderous, and completely unethical. In fact, his appearance in the Bonus Dungeon of the original game involves him Breaking the Fourth Wall and describing all of the terrible things that the developers themselves said about him during development. However, a combination of outrageously hammy dialogue, character design that makes folks think "evil Harry Potter" and being a Purposefully OverpoweredSecret Character in the bonus dungeon results in way more fanfics pairing him with the center of his stalking than there should be based on his canon personality (said personality resulted in his appearance in the second game making him into the Big BadFinal Boss).
GLaDOS sometimes gets this as well. While most of her fans embrace her evilness and love her for it, there are also those who completely ignore her murderousness and reduce her to a somewhat bitchy, but ultimately goodhearted, Deadpan Snarker. This is often done in the name of making their favorite ships more plausible.
Dr. Steinman and Sander Cohen from BioShock have tons of fangirls, in spite of them both being basically serial killers who horribly mutilate people for fun. Same goes for Frank Fontaine/Atlas, an amoral gangster who takes advantage of hundreds of innocent Rapture civilians by introducing them to addictive, physically disfiguring Psycho Serum, and profits off of war and conflict. Apparently, all it takes to get around any of these crimes is to look handsome in their radio message portraits.
Similarly, Daisy Fitzroy is turned into a martyr by social justice warriors who find the game and its message of non-extremism racist, despite her having tried to kill both the main characters when she no longer found any use for them and threatened her cult of personality, following it all up by trying to kill a small boy.
Daisy Fitzroy has been negated due to the revelation in Burial at Sea that she didn't want to kill Fink's son in the first place, and argued with the Luteces when they told her the plan. She only went through with it as Elizabeth killing her would cause her to develop from a girl to a woman, and even though she would not live to see the revolution succeed, she knew that Elizabeth and Booker would win.]]
As of Burial at Sea, Atlas has lost all love from the fandom due to crossing the Moral Event Horizon several times, his first big one by trying to do a trans-orbital lobotomy on Elizabeth, and threatening to do the same to Sally. The one that made the entire fandom turn against him was that, at the ending, he mercilessly beat Elizabeth to death with a wrench while shouting at her for information. Worse was that he didn't really kill her, causing her to suffer badly at the end.
Both of the Elibe villains from Fire Emblem, King Zephiel and Nergal, get slapped with this treatment a lot. Both do have horrid pasts - the former (as Blazing Sword shows in one chapter) has Abusive Parents, with the mother ignoring him and the father having nearly murdered him twice, and the latter used to be a good shaman and family man before being corrupted by the dark side. Zephiel winds up waging a massive war against the whole continent with the intent of wiping out humanity, and Nergal wants something similar, except that he also wants to control dragonkind as well. But to a part of the fandom, they're only victims of the cicumstances and not responsible for anything.
Hatoful Boyfriend fandom has a degree of this towards Iwamine Shuu. Monstrous as his actions are - cutting off the heroine's head and boxing it so her childhood friend can open the box and see it is the least of it - most of fandom's focus is either on how cool blood apparently is or on how he crushed on someone who died without ever returning his feelings years ago and isn't over it.
The second game brings us The King. Many fans won't even acknowledge that he does anything wrong - and he does a lot wrong - because his backstory is genuinely terrible. They also won't acknowledge that he had some responsibility for his own fate.
Fangirls of Metro Last Light are sometimes a bit too fond of Pavel. Yes, he's something of an Anti-Villain who's more honorable than his fellow Red Line soldiers, but they all too easily forget the fact that he unrepentantly stabbed Artyom in the back and betrayed him to the Reds, doing nothing to stop his subsequent torture and interrogation, and from there proceeds to carry out his part in Korbut's genocidal plan without a single hint of hesitation. Yes, he shows some remorse when fighting Artyom in Red Square, but in spite of all his talk of mercy, he never actually stops doing any of the nasty stuff he does. As far as his fans are concerned, all it takes to absolve all of that is a pretty face and a sexy Russian accent.
Nagito Komaeda of Super Dangan Ronpa 2 has intentionally tried to set up his own murder by more or less forcing another student to take action under the assumption that Nagito would have killed someone had they not (which ultimately failed because you just can't rely on anyone these days), set up a plan to get everyone killed after finding out they were part of SHSL Despair, showed no remorse for doing so, accidentally got Chiaki Nanami (the one person he was trying to save, as she was the only one innocent of all crimes since she was only an AI student and not actually a part of SHSL Despair) killed in the process, and sided with the culprit on occasion. However, people often fall into the trap of his character arc by unintentionally making him out to be inherently terrible when he's the perfect blend of this trope and the opposite end of the spectrum - if you aren't downplaying his villainous side, you're exaggerating how terrible he is. Many fans either really hate the guy, or excuse his actions entirely by citing his tragic past, specifically his frontotemporal dementia as the be all, end all reason behind all his actions.