Ao Oni has this with Megumi/Mika. In Version 1.0, she was still in love with Takuro (and they were an Official Couple), but with streaks of Cowardly Lion and Genre Savvy (ie she is aware enough of her barricade's weakness to order Hiroshi to lock the door when he enters and leaves). In Version 6.23 (the latest version) all she does is berate Hiroshi for thinking she'd go around the mansion with the monster still running around, then mutters "Takuro..." under her breath every time she's spoken to afterwards. Then she dies.
The Ar tonelico series features an in-universe example. Any part of a Reyvateil's problems, desires, or what-have-you get blown to spectacular proportions in their Cosmospheres. Outside of the Cosmospheres, however, the changes in character after you go in to their Cosmospheres are much more subtle.
Achmed Khan from Backyard Sports was originally a great athlete who simply listened to rock music (although he had his headphones on everywhere). This quirk was run into the ground by later games, making him a guitar-wielding crazed fan, down to the fact that he could not focus due to loving music.
The whole of Command & Conquer: Red Alert has undergone this. While some people complained that Red Alert 3 was ridiculously over the top compared to the previous games, it had already drifted dramatically starting with Red Alert 2. Red Alert had time travel, an Action Girl, and some over-the-top technology and characters, but it was about as serious as the Tiberium Series. Red Alert 2 expanded on this with much more over the top stuff (Giant mind controlled squid?) and pulpish units and scenarios. But the developers of Red Alert 3 focused much more on the cheesy elements.
Command & Conquer: Tiberium Series also has undergone this, if more subtle. The first game was a quasi-futuristic military strategy of the western nations against an elusive terrorist faction with stealth and laser technology. The second game threw the world into chaos, added jumpjet infantry, mecha, cyborgs, mutants and a super AI and attempted to explain Kane's origins. The third game went back to the original style, but left the super tanks, super weapons, lasers, stealth, and added mobile defense posts, Ninja, mad suicide bombers, and all sorts of walking, hovering and flying aliens, who subsequently got their asses kicked. The expansion of that game then re-added the mecha and cyborgs. The so far last game threw away base building and money and added Powered Armor to everyone, while extrapolating nearly all unit concepts introduced in the series into one game. Talk about a Zigzagged Trope.
Essentially all of the cast in the Crash Bandicoot franchise have devolved into dopier, more sociopathic caricatures of themselves. This says nothing of the series' cultural nods; Crunch for example went from a somewhat aggressive tough guy with subtle demeanor and voice mannerisms as a slight homage to Mr T to basically being a shallow parody of the star. Even former 'sane' straight men like Aku Aku and Coco are now melodramatic jerkassgenius ditzes.
The Disgaea series always bring back the characters of the previous games as bonus characters. However, they always come back as flanderized versions of themselves. The ur-example is Laharl, the protagonist of the first game. He starts out as an annoying, self-entitled brat but goes on to deal with a potent childhood trauma, stops shutting out his feelings, gains devoted allies, and even a Love Interest. He's still kind of a jerk at the end, but you can tell he's matured. When he appears in the sequels he's still the Overlord, but he acts like a annoying brat who wants to be the main character again for more screentime and related benefits, such as being able to win every battle because the player can just reset and grind more until he wins.
Etna starts as King Krichevskoy's vassal, who, after the king's death, is given the mission of raising Laharl. Long story short, she starts off loathing the prince for his brattiness but gains respect for him as he matures, and eventually settles into being his right-hand demon. Cue Disgaea 2, where she leaves Laharl's service in a quest for personal power because she hates him. Then there's her fondness for sweets; while her sweet tooth is mentioned once or twice in the original, some later games (e.g., Prinny: Can I Really Be the Hero?) depict her as sweet-obsessed in search of some legendary dessert. Her A-Cup Angst also got blown out of proportion, from a single scold at Laharl for mentioning that she doesn't trigger his "sexy body weakness" to being completely delusional about having a "nice body" and constantly arguing about it with Flonne.
Mao always had a Mad Scientist vibe going on (even achieving ecstasy by doing "experiments" on his subjects), but in his game his main quest was to deal with his supressed memories of causing his father's death, kill his father's murderer and become ready to be the next Overlord and finally letting his father's soul rest. In the later games he is still the Overlord, but all he does is look for subjects for his experiments and moan in pleasure just by thinking of what he could do with them.
Disgaea D 2 reveals that Laharl has not lost his Character Development, and he's still more mature than he seems, bonding with his sister Sicily, worrying about Etna, and eventually impressing the Krichevskoy Group (who believe he is an Inadequate Inheritor) enough to accept him as Overlord. Everyone's first impression of him is still that he's a tiresome brat, though.
Oghren suffered this in Dragon Age: Origins – Awakening. In Origins, his alcoholism and Boisterous Bruiser antics were all a front for the depression that seized him after he lost his wife, entire family, and whatever status he had in Orzammar. In Awakening, he forgets whatever lessons he might have learned during his travels with you and signs up with the Grey Wardens simply so that he can continue to drink, fight, and party it up, ditching his current family in the process, and all of his antics are Played for Laughs.
Yuan Shao is originally portrayed as an honorable, if not a bit too proud, nobleman with some Small Name, Big Ego tendencies. As the series progresses, his prideful characters has been exaggerated to the point that he became extremely arrogant and pretentious. Which might be more or less accurate on his 'real' persona base on Guo Jia's comment on him in Romance of the Three Kingdoms (the source material).
Though on that note, it's worth mentioning that Guo Jia was at the time basically writing a propaganda piece to counter Yuan Shao's own against Cao Cao (Guo's boss), so taking it with a pinch of salt might be called for. Besides, Romance itself had a bit of a tendency to flanderize the historical characters it was borrowing, for the sake of telling an entertaining, cohesive narrative.
No one got it worse than Zhang He. In 3, he was somewhat flamboyant and his dress and weaponry were based on Vega/Balrog from Street Fighter. That's it. By 5, he's gone so overboard in both speech and mannerisms...he can barely go two sentences without "beauty" or "grace"...he's actually become fruitier than the real Vega/Balrog!
Done on purpose to the Brotherhood of Steel in Fallout. From Fallout 1 to Fallout 2 they become significantly more secular and generally bigger Jerkasses, then even more so in Fallout: New Vegas. This is due to the time differences between the games, as each generation drifts further and further away from the original intentions of the organisation and into more overt technology worship and becomes increasingly secular and elitist, which was originally a very minor aspect of the BoS. Their increasing elitism is a major plot point for their quest line, including the member that can be recruited by the Courier. In the NCR and Independent endings, their decision to embrace or abandon their isolationism ultimately decides whether or not the Mojave chapter even survives.
There are, of course, a few Chapters that have completely different kinds of flanderization. Naturally, the Flanderized "White Knight" version actually started to expand and likely is now more powerful then the entire OG Brotherhood combined. Minus their giant propaganda robot, even.
When Mai Shiranui was first introduced in Fatal Fury 2, she was simply a female Ninjutsu master whose relation with Andy Bogard (being the granddaughter of his sensei, Hanzo Shiranui) was barely mentioned in her backstory. In later games (especially in the anime adaptations), she became so fully obsessed with Andy to the point that she yells his name whenever she gets K.O.ed in The King of Fighters games, one of her intros involves scaring the crap out of Andy with a baby handpuppet and most of her endings revolve around her trying to get Andy to marry her.
Mai's voluptuousness in Fatal Fury 2 and Special was also nowhere near as exaggerated as it was in later games. It wasn't until the KOF games, when they gave more revealing clothing and bouncing breasts, that her status as Ms. Fanservice was cemented, with heavy contribution (pun intended) from Masami Obari via the Fatal Fury anime films.
In Final Fantasy VII Cloud Strife actually did very little brooding, preferring to focus on fighting Sephiroth and saving the planet from Shinra. The guy even cracked a few jokes at his friends and could take a jab back in return, and is very caring of his friends and claims he "trusts everyone". His archrival Sephiroth was a Dark Messiah who wanted to become a god to reshape the planet into his own personal utopia, and he screwed with Cloud's head to do it in revenge for Cloud defeating him years prior. Ever since the original game Cloud has been warped into a loner who brushes off his friends' attempts to help him while he broods and angsts over Sephiroth, and Sephiroth's only character traits now are his ability to manipulate Cloud's emotions and taunt Cloud with the fact he's so good at it. The Foe Yay between them has also gotten increasingly heavy-handed, to the point Sephiroth almost seems more like a jealous stalker or a scorned ex than Cloud's hated enemy.
There's a common fan-theory going around as a result of the Flanderization that Cloud was afflicted with the "Sadness" status ailment in Advent Children, up until the ribbon he was wearing was revealed, since Ribbons remove all status ailments in the series. The Flanderization was reversed in Dirge Of Cerberus, where from what little we see of him, he's a total absolute Badass. Looks like he got his wish. Too bad the game didn't do too well. The actual explanation is that people suffering from Geostigma, which Cloud had for most of the movie, suffer from intense depression; either from the disease itself or the fact that it's incurable and will kill you.
There's also Aerith and Yuffie. Aerith was originally a headstrong Plucky Girl with a strong spiritual side and a slight flirtatious streak. The girl threatened to rip off a guy's balls at one point. In the spin-offs whatever stubbornness and flirtatiousness she had is gone, and her spiritual powers and connection to the planet have become her core character traits—as a result the girl is portrayed as a saint, the human incarnation of Incorruptible Pure Pureness with powers so strong she can save the world from beyond the grave. Meanwile Yuffie was originally a bit goofy and silly, but she was still quite cunning, witty and sneaky—she is a ninja after all, and the former Trope Namer for So Long, and Thanks for All the Gear. In spin-offs she's a typical Genki Girl and is just loud and hyper. Crisis Corerectified both of these though; and Aerith and Yuffie are more or less back to how they were in the original game.
Not to mention a lot of fans Flanderize the characters, thanks to Poe's Law. Playing the original Final Fantasy VII, you might actually be surprised to find that Cloud is NOT eternally whining and brooding, or that the characters actually DON'T cry as much as the Hatedom say they do.
And there's also Terra Branford from Final Fantasy VI. In the original game, she was a bit unsure of herself and afraid that she'd never feel love, but she still wasn't afraid to fight for the Returners' cause and stand up to Kefka. Dissidia turns her into the ultimate deer in the headlights, and she's completely afraid to fight at all. She's strictly this timid little girl with little of her characterization from VI, to a point where she doesn't even use her sword outside of chase scenes so they can have her fight with magic from the distance. Worse, it takes the advice and bodyguarding of two younger males for her to start regaining some element of her original character.
Final Fantasy X-2 has a similar example to Yuffie with Rikku. Originally, while always hyperactive and eccentric, she was genuinely intelligent and witty, especially considering she only fifteen. Once the sequel hit, hyper seemed to be the only trait brought over. All her wit and intelligence disappeared nearly entirely because the writers seemed more content to make dumb blond jokes, with all the wit given to Paine, the Deadpan Snarker character created for the sequel to team with Yuna and Rikku.
Though it's kind of justified, since Rikku no longer had to worry about her cousin sacrificing her life for a cause that'd bring peace for a few years only so now she could live her life without many worries.
Sodom from Final Fight was originally a samurai-themed underground wrestler with a somewhat misguided fascination with Japanese culture. In the Street Fighter Alpha series (especially in the Japanese versions of the games), this fascination became more of an obsession, with Sodom usually speaking in mangled Japanese, writing his gang's name in kanji, and going as far as to travel to Japan to recruit sumo wrestlers for his gang.
Kratos of God of War. In the first game, his bloodlust is a facet of his deeper personality - he channeled the memories of what he had done into his rage to become more brutally efficient. In the second game, Kratos lost that, and became simply bloodlust and badassery in human form. The third game, however, reverses this trend thanks to his interactions with Pandora - it is through her that he is reminded of the importance of hope, which allows him to forgive himself for the sins (at least with regards to killing his own family) he committed.
All the Harvest Moon 64 characters were either flanderized or made Lighter and Softer for Back to Nature. The Harvest Moon: A Wonderful Life characters descendants were flanderized even more so for the DS games, but that's justified due to them not being the same people. For example Popuri was originally just The Ditz and was a bubbly sweetheart, if not a bit naive. In Back To Nature she became an immature Woman Child, which only got worse with her appearances in both DS and Island of Happiness where she also seems to have taken some hits to her intelligence.
Also done with his unusual speech pattern. In the first game the "Definition:" or "Statement:" or "Query:" before his dialogue was relatively simple, there weren't that many of them (maybe five or six at most) and they served to logically categorize the things he said. In KotOR 2, the prefixes start becoming increasingly specific. The HK-50s take it to the next level by adding descriptive adjectives to the mix, to the point that they often serve to ironically undermine the following statement completely, a la Stephen Colbert's "The WORD" (i.e. "Hasty Retraction:", "Condescending Explanation:" or even "Fabrication:".)
Possibly justified: at some point between games HK-47 was damaged to the point where the Exile had to rebuild him almost from the chassis up. The prefixes thing can be explained by you taking most of the parts to repair him from destroyed HK-50's.
Left 4 Dead 2 exaggerated the traits of the survivors within The Passing campaign DLC. Coach may sometimes hope that a Burger Tank restaurant will be open or be reminiscent of a boiled peanut festival. Rochelle, who was mildly snarky in the game, is now full of snark in The Passing. Ellis' stories grown more ridiculous, such as how his friend ate two pounds of raw chicken. Nick, who doesn't like to be covered in dirt and grime, became borderline fearful of germs (he may ask the other survivors to carry him above the sewer water) and states that the entire Zombie Apocalypse could have been prevented by everyone using more hand sanitizer.
Inverted with Ganondorf. In the first two games he starts out as some sort of boar/pig monster, in The Legend of Zelda: A Link to the Past he was revealed to have once been a thief who wished for power, in The Legend of Zelda: Ocarina of Time it is revealed he was a human wizard, but came off as an unruly and savage power hungry tyrant. In Wind Waker he is depicted as intelligent and sophisticated, and despite the controversial insertion in Twilight Princess, that was his most eerie and intimidating appearance of all.
Reverse-Flanderization has happened to all of the cast as we go from the short flavor text in the manual to actually being able to act as real characters within the games themselves. Ganondorf goes from generically evil to quite sympathetic: he wants to take over Hyrule because his people lived in an arid desert, barely surviving the day's searing heat and the night's bone-chilling cold. (Mind you, this doesn't jibe with Ocarina of Time, where The Dark World was a future where he'd taken over and not, well, the Dark World. A paradise for the Gerudo is not what he created.) Zelda goes from "Kidnapped at the beginning, rescued at the end, has one or two lines" to a character who is wise, has psychic dreams, sometimes is sole ruler despite the title, and Minored in Asskicking; the obligatory kidnapping is shorter every time. Tradition says Link will never get to speak, but we see more and more of each incarnation's life before the adventure. The Wind Waker even gives his dialogue options more length and flavor than simple yes-or-no answers.
Inverted in the Mass Effect series. In the first game, we see few members of each species, each playing up one identifying trait (belligerence for the krogan, devotion to duty for the turians, the like), but in Mass Effect 2 we meet and talk to many different members of each species with widely varying personalities and outlooks, giving us a much broader look into the societies built around the identifying traits from the first game and the kinds of people that live in them.
Urdnot Wrex de-Flanderizes pretty significantly for his appearance in Mass Effect 2. In the first game, he states flats how the Krogan mindset has coupled with the genophage to mean that his people are dying out—mostly due to work as mercenaries and bounty hunters being more appealing than working on a solution. He spends the majority of the first game idly complaining about the Krogan's problems, but doesn't really do anything until Virmire, in which he's mostly just belligerent. Cut to Mass Effect 2, where he's revealed to have spent the last two years forcing the Krogan to address the problems caused by the genophage before the damage is too great to be undone. While everything he does is in typical blunt Krogan fashion, his actions and goals take on much broader scope during the second game.
It seems this subversion is actually intended. While all species continues to get flanderized throughout the series, Shepard's own team continues to defy their species' Planet of Hats. Wrex and Grunt are not unthinking berserkers, Garrus is a maverick who is willing to go against law and order, Mordin actually has scientific ethics and is willing to look at consequences beyond a few short years, Thane being the opposite of an assassin in Mass Effect 3, Tali willing to put aside her race's racism towards synthetics, Legion willing to engage other species rather than remaining in isolation, etc...
Conrad Verner is Flanderized a fair bit between 1 and 2. In the first he's just a harmless fan (even described as such by the Journal) who wants an autograph and a picture of Shepard, and has a romanticized view of life as a Spectre. In the second he's bought himself replica armor and is trying to shake down a bartender for the deed to the place. Come to find out that over the last two years he's been obsessively copying everything Shepard used to do, and fancies himself a vigilante working in Shepard's stead.
This is purposely invoked in the Citadel DLC, which is essentially a Fanservice Pack full of in-jokes and past references to let the fans have some fun with their squad one last time. It plays up a lot of the squad's minute character quirks or brings up one-off jokes like they're a regular trait of that character's personality. For example, Tali gets absolutely hammered at the house party, despite having only been explicitly drunk at one other point in the series. Wrex seems joyously happy to be fighting alongside the squad again, compared to his normal grumpy attitude. Garrus even lampshades his own obsession with calibrations, promising to stop mentioning them if Liara stops saying 'by the Goddess.'
Mega Man X: As Executive Meddling forced the series to go beyond the creator's planned ending, X5, some of the main characters had certain aspects of their personality stretched out to artificially create conflict for the next few games. While Zero always stayed friendly to X, he became rather gruffer and more stereotypically badass as the series went on, especially when Axl was introduced. Sigma degenerated just as badly as Dr. Wily, if not worse, as he went from very nearly destroying the world and being a truly Magnificent Bastard...to a shivering pile of zombie-animated debris in just one game, and by the next game explained hisfinal boss status as simply "because I'll never stop until you're dead!" (It should be noted that it's been hinted that, as Sigma's bodies are destroyed, a little bit of him truly dies. This would be why, by X6, he's barely sane and can't think of anything besides killing X. This is why his form is that of some grim reaper zombie thing.) It was X that the fans complained about the most, though: while he had always been more pacifistic and less violence-inclined than Zero, this was expanded into the defining aspect of his personality, so that rather than being a reluctant cop, he was a stereotypically annoying whiner who kept advocating non-violence even when the situation had clearly gone south. This led to him abandoning active duty at the beginning of X7, so we started off playing a Mega Man X game without playing as Mega Man X.He does return, though.
Speaking of the X series, even words can undergo Flanderization. The term "Maverick" initially referred to a Reploid who attacked and killed humans as a result of Wily's Maverick virus, but starting with X4 the meaning started to become warped as a political tool, usually with the purpose of sending the Maverick Hunters after the designated targets. The distortion of its meaning remains long into the Zero series, where the Resistance are (mostly) law-abiding Reploids just trying to keep themselves operational amidst an energy crisis. Most of the damage has been reversed in the ZX series, but with Albert dead and Mikhail (likely) soon to join him, it's only a matter of time before Thomas makes history repeat itself. Though this Flanderization of "Maverick" could be interpreted as similar to the US's Red Scare, making it a more in-universe example. This would make sense, as the reploids (robots) get more and more intelligent and more sophisticated motives begin to appear, sophisticated fears based on treason and betrayal breed distrust and suspicion, logically leading to the use of "maverick" as a political tool.
Snake and cardboard boxes got out of hand at some point... Scratch that, they were always out of hand, it simply became more and more obvious as the series went on. According to Word of God, this was an elaborate Take That to the NES Metal Gear, where the cardboard box was basically a Disk One Nuke that let one stand in front of guards and even shoot them without a silencer and without setting off the alarm. For instance, by Metal Gear Solid 3: Snake Eater:
Snake: I dunno, I was just looking at the box, and suddenly I got this irresistable urge to get inside. No, not just an urge - more than that. It was my destiny to be here; in the box. Sigint: Destiny...? Snake: Yeah. And then when I put it on,I suddenly got this feeling of inner peace. I can't put it into words. I feel... safe. Like this is where I meant to be. Like I'd found the key to true happiness. ...Does any of that make sense? Sigint: Not even a little.''
In Super Smash Bros Brawl, Snake is first revealed at E3 by getting out of a box. He is first revealed in the adventure mode by getting out of a box. Every character has three different taunts. Snake's up taunt is getting into a box. His side taunt is getting into a box. His down taunt is getting into a box. It's not just developer laziness either; all three have him do it differently.
In the first few Monkey Island games, Guybrush had a tendency to be a bit dim every now and then, but overall proved himself to be a fairly competent adventurer. In the first game, he's pretty much by definition the most courageous and competent character in the game (aside from Elaine), as he's the only one willing to challenge LeChuck, and earns every step he makes on that path. By the time Escape from Monkey Island happens, it's a wonder he can even put on his own pants, let alone solve any of the game's puzzles.
The humor in the games is also Flanderized quite a lot. The first game is actually fairly serious with a parodic atmosphere. The second game amps up the anachronism, which goes Up to Eleven in the ending. Since then, the games are pretty much run on Rule of Funny.
Johnny Cage became so diluted he became a parody of what he strove not to be. In the beginning he was more serious (but no less arrogant) and a very competent fighter, but devolved into a Plucky Comic Relief character as the series went on. This was likely a Take That directed at Daniel Pesina, the actor who originally played Johnny Cage, after he had posed in character as Cage to promote another company's fighting game (Blood Storm).
Inverted in the case of Nightwolf. Originally a parody of Thunder Hawk in Mortal Kombat 3, he became The Smart Guy in the cartoon, and in Deception, we had him literally going through hell to rescue Liu Kang. Then in Mortal Kombat 9 he became the leader of the Defenders of Earthrealm.
Sadly played straight with Mileena who has been completely flanderized into a Psychopathic Woman Child in MK9.
Actually beneficial in the cases of Sonya Blade and Jax, as well. In their debut games, they were written as Special Forces members, but their looks and skillsets had absolutely nothing to do with any of that. As the games progressed, they gradually became what they were actually supposed to be, getting appropriate gear, skillsets, and weapons. Though in the case of Jax, it could be argued that this is a bad thing, as his gear and weapons have gradually begun muscling in on the gear and weapons of Stryker. Particularly in Armageddon, where they had identical machine gun attacks.
Persona 4 has this in-universe with the characters' Shadows, which reduce them to a single defining (and completely overblown) character trait.
More specifically, it takes their Fatal Flaw and grossly exaggerates it. Chie's takes her need to control Yukiko to feel better about herself and becomes a straight-up dominatrix, Kanji's takes his insecurity about his girly hobbies and becomes absolutely flaming, and Naoto's takes her need to act more mature for her age and frustration about her gender and becomes a human-sized kid's toy, switching between overblown dramatics and childish temper tantrums, and is obsessed with giving Naoto an "operation".
Chie's love for beef gets exaggerated in Golden, however.
Akihiko Sanada in Persona 3 is mentioned to only eat 'things with protein shit' about... once. By Persona 4 Arena, his nickname contains 'Protein Junkie', and he's ordering Protein everywhere nonstop and talks more about protein.
His protein obsession is mostly Played for Laughs; an arguably less funny trait that got blown up is his Blood Knight tendencies. Those who played Persona 3 know that curbing his obsessive desire to fight was an integral role in his Character Development, starting in the wake of the death of his best friend Shinjiro, and from that point onward, he'd mainly fight for the sake of those he cared about. In Arena, he's fresh off the heels of a world expedition, driven from his obsessive need for getting stronger, and it's also stated that he dropped out of college to do it. While his story mode ending mentions that he wants to become a police officer, seeing him as battle-happy as he was at the start of his game is still jarring.
The Numans/Newmans of the Phantasy Star series have undergone a race-wide flanderization of their own; they are now often sardonically referred to (and mistaken for) Space Elves, due to Sega focusing more on their adeptness with magic and their elflike appearance:
In the original quadrilogy, Numans were originally genetically-engineered Half-Human Hybrids as an expy of Myau the Musk Cat in the first game (Nei from Phantasy Star II was originally going to have far more catlike features and a tail, according to Tohoru Yoshida).
By Phantasy Star Online, Numans were renamed to Newmans and made into a full race of genetically engineered beings rather than one-off experiments. PSO made them more like a Witch Species, as they were considerably better with Techniques than Androids or Humans of the same class.
Captain Qwark from the Ratchet & Clank series started out as a reasonably intelligent character who was simply past his physical prime and a glory hound, with implications that he had once actually been a legitimate hero but had soured as he'd gotten old. In the second game, Qwark successfully takes control of the Mega Corp. corporation and executes a Evil Plan that only fails when he puts the batteries of the Helix-O-Morph in backwards (it's a long story). The third game has him pull a Heel-Face Turn and begins his transformation into The Ditz, with his stupidity, cowardice and glory-seeking tendencies played up to such a degree that by the time of Tools Of Destruction he bears almost no resemblance to the calculating villain from the first two games. His tendency to exaggerate stories has also become progressively more absurd. The first game's characters are all subject to Early-Installment Weirdness, but Qwark is the most prominent example of a complete rewrite in personality.
Notably, Qwark seems to be exceedingly competent when playing the villain, as all of the stages personally designed by him are among the hardest in all of the games they appear in. It's only when he's trying to be a hero that he's incompetent.
The Rabbids from Ubisoft's Raving Rabbids franchise have been greatly Flanderized. In the original Rayman Raving Rabbids, the Rabbids, although somewhat dimwitted, were a major threat to Rayman's world and the human world, often enslaving innocent creatures, locking Baby Globoxes in cages and attacking humans with toilet plungers. Since Rabbids Go Home, the Rabbids have gone from being Chaotic Evil yet dimwitted to being complete morons and entirely chaotic. In Rabbids Invasion, their evil side is almost compeletely missing, and their stupidity is even bigger. This can be proven since in the games, the Rabbids know how to fly spaceships while in the show they can't even insert a coin in a photo booth.
In the Rayman series, Globox had a huge Flanderization. In Rayman 2, he's not a bright spark but he's still rather rational and helpful to Rayman. Sometimes, he acted clumsy. Since Rayman 3: Hoodlum Havoc, his clumsiness and his stupidity grew out of proportion and he became a millstone round Rayman's neck.
Girl Stinky went from being a Wrongly AccusedSmug SnakeKnow-Nothing Know-It-All who was nonetheless friendly enough with Sam and Max to help them out a few times (or at least look the other way while they did what they had to do) in Season 2, to being psychotically evil and cripplingly lazy in Season 3. Also, in Season 2, the other characters consider her reasonably attractive despite her awful personality, and Flint Paper thinks of her as a Film NoirFemme Fatale, but by Season 3 her personality leads her to be considered so repulsive Max nearly projectile vomits after watching her and Sam do a Fake-Out Make-Out. Since the universe functions on Rule of Funny, this is generally considered an improvement.
Max's childlike aspects were exaggerated between the comics and Hit The Road, but he became a full on manchild in the animated series, which was used for the Telltale Games as well. In the comics, he's still whimsical, but also snarky, intelligent and tough, and his moments of childish behaviour are mostly based on Steve Purcell's own memories of himself as a child and all the cuter for being assigned to a more mature and competent character. By Season Three he can use Psychic Powers by using special children's toys, which 'only work for those with the mind of a child', and his snark has mostly gone in favour of creepy, deranged glee and references to his stupidity and short attention span. It works a lot in Sam's favour, though, by giving them greater Cast Speciation - decreasing Max's snark frees up Sam to become a Deadpan Snarker, rather than a toned-down version of Max like in the comics.
However, in Season Three, after switching to Max, the game shows a random image of something from Max's memory. Many of these things include images of things in American history or various animals, suggesting that Max is smarter than his personality lets on.
As some have pointed out, the animated series has many episodes, and as such has far more back story info in it than the comics or Hit The Road do. It was inevitable the Telltale team would turn to it for inspiration. Max was obviously toned down for kids for the animated series, but there were plenty who said his personality in Hit The Road was too serious in comparison, so it worked out.
Sam himself, whilst always being the straight man to Max's insanity, started off as Max's best friend and had turned far more into a father figure by the later Telltale Games.
Most of the characters in the series have suffered this at some point not long after the release of Sonic Heroes and Sonic X. (Surprisingly, Dr. Eggman is one of the only ones who hasn't experienced too much of this.)
Amy Rose is a perfect example, having gone from being a cheerful and slightly head-in-the-clouds girl, to overly and overtly obsessed with Sonic, sometimes in borderline violent ways.
Blaze has actually gone through de-Flanderization; in Sonic Rush she was an icy loner who constantly stressed not wanting anyone's help, she was somewhat more mellow in Sonic Rush Adventure, and nowadays she's just a fairly shy and formal character.
In Knuckles Chaotix, Espio the Chameleon was a detective and had the ability to walk on walls and ceilings. In Sonic Heroes, he was given more personality and also had some ninja elements to them due to his previous abilities, plus the fact that he should have invisibility, due to being a chameleon and all. It seemed more like a hobby than anything major. In Sonic Generations, Espio's ninja qualities have been enhanced to an obvious degree, with more ninja mannerisms, a heavier focus on his invisibility and shuriken, and his voice sounding like it was ripped straight from the animes.
Not to mention Shadow the Hedgehog in his own game: in Sonic Adventure 2, yes, Shadow did partake in some minor brooding, but that wasn't a primary character trait. Much like Cloud Strife in his original appearance, he could make a joke, he could take a joke, and he didn't care about his hazy past, all he cared about was accomplishing his current goals (thinking about it, they're actually eerily similar). However, in Shadow the Hedgehog, Shadow would never stop brooding and pondering about his past. However, once he learns about his past, that apparently satisfied his ponderings and relaxed into a characterization close to his original.
Xiba from Soulcalibur V's love of steam buns is noted a couple times in the game, usually before a match/after winning. In most fanfictions and other fan works, however, his love for food overshadows all other parts of his personality, to the point where that is the only thing he ever talks about when he has dialogue.
Welch Vineyard of the Star Ocean series. She originally appeared in Star Ocean 3 as the energetic and somewhat tsundere item creation clerk. She was popular, so she returned as a hidden recruitable character in the remakes of Star Ocean and Star Ocean 2, as well as returning to a role similar to her Star Ocean 3 role in Star Ocean 4. (albeit looking a little different in the latter) Her later appearances saw her randomness, tsundere-ness, and energy level turned way up, making her a little obnoxious at times.
At some point, the internal struggle with the Satsui no Hadou dominated Ryu's when it was retconned into his backstory as the reason he beat Sagat and scarred his chest whereas it was not mentioned once in Street Fighter II (Albeit because said story hadn't been written yet.) Street Fighter Alpha is a prequel to II and introduced said plot point as well as integrating Ryu's story into Akuma's. Street Fighter III has no mention of it but by Street Fighter IV, the Satsui no Hadou has become the most important aspect of Ryu's plot despite him overcoming it to the point where Gouken's ending in the original IV is about Ryu being corrupted briefly as well.
Peach is largely known nowadays for her over-the-top stereotypical female personality and ditziness, but she wasn't always like that. The series started off with her having the power to undo Bowser's evil spell which is why Bowser kidnaps her (at least, according tothe game's instruction manual). Still, in Super Mario 64, she was portrayed as a dignified, intelligent-sounding monarch. Come Super Mario Sunshine, her ditziness took over full force, leading to the Peach we know today.
Bowser himself has also gone through some personality changes over the years. He started off as being someone who wanted to take over the Mushroom Kingdom, take the princess, and beat Mario, to becoming a tough guy with an image to keep and would be rather be caught dead than to assist Mario in some of the RPG spin off games. He goes down even further by kidnapping the princess (and possibly taking over the world/galaxy) because he likes her and finds fighting Mario more of a sport rather than a need to get rid of someone standing in his way for total domination.
The most notable example of Flanderization regarding him can be found in the Mario & Luigi series. In the first game, he had very bad luck, and wasn't as brave as Mario, but he was still capable enough in his own right. In later games (particularly Partners in Time), he's a complete wuss who can't seem to do anything without screwing up and getting hurt.
Luigi's cowardice could be a case of Canon Immigration, as even back in the western cartoons Luigi was shown as easily rattled and averse to conflict, whereas Mario never backed down from a challenge. One could consider this a cross-continuity case of Flanderization. In the cartoons, Luigi was generally more emotional than Mario in all aspects; cowardice, depression, anger, impulse, hamminess... The games decided to just latch onto cowardice and run with it from there.
This has also happened to Princess Daisy of all characters. After her much-needed Divergent Character Evolution away from Peach, Daisy became more of a tomboy with a spunky and energetic side, but was still generally soft-spoken and rather calm. As the games went on however, Daisy became more hyperactive, louder and more shrill with each new appearance. Needless to say, this hasn't workedout too well.
Another character who got flanderized is Toadsworth. In his debut game, Super Mario Sunshine, he was understandably worried about Peach, but remained somewhat level-headed about it. By Mario & Luigi: Partners in Time kicked in, he became overly paranoid, to the point of assuming his past selftransformed Peach into an infant and kidnapped her the second he saw him with Baby Peach. However, in this case it turned out for the better, since he didn't have that much of a personality in Sunshine.
Veigue from Tales of Rebirth gets this treatment whenever he appears in one of the Tales comedy CDs. In the game, he has a habit of saying or yelling his girlfriend's name a lot, and occasionally gives melodramatic equality speeches, but they're hardly his only character traits. In the CDs he becomes "That guy who yells his girlfriend's name and gives melodramatic equality speeches".
Paul Phoenix has gradually become more of a joke character as the series has progressed. He remains one of the toughest characters in the game, however. Kuma began in Tekken 1 as a fearsome and realistic bear character but began to become a joke in Tekken 2. His identically named son who appears from Tekken 3 onwards is a complete joke character due to the introduction of Panda.
Likewise, Marshall Law too. His story was fairly realistic in the earlier game, trying to expand his business into dojo, having it trashed by Baek and learning to let go of revenge. Then Tekken 4 happens and he fell into poverty and trying his best to win the tournament to ensure his family is well-fed. That was the point that Law takes a downward spiral into a Joke Character like his buddy Paul as 'being in Perpetual Poverty' becomes his secondary gimmick aside of being a Bruce Lee Clone, and he also proves himself to be Not So Different with Paul in terms of wackiness, especially when you compare his ending in Tekken 2 where Law made it clear that he's much less cocky and dignified than Paul (succeeding in flip kick when Paul fell flat to his face).
Yoshimitsu is another good example: He started out as simply a man, in a suit of armour, armed with a katana. Now he is armed with twin lightsabers, a spinning hand that lets him hover like a helicopter, insect wings that he keeps stored in his back, an active camouflage system and all manner of various unnecessary and probably quite inconvenient additions to his costume (which incidentally has now morphed into fully fledged power armour) such as a beetle horn on his head on 4, strange hanging-rope things in 5 and 6 and an absolutely huge entirely useless metal halo welded onto his back in Tekken Tag 2. Oh and if we take his endings as canon, he apparently can now also cast magical spells such as the ability to cast an after-image.
Lara Croft started as a modest, down to earth woman in Tomb Raider. In Tomb Raider 2 she became more witty and slightly more threatening and bloodthirsty. Later on she was heavily Flanderized into a Hollywood-style tough girl for Tomb Raider: The Last Revelation, and by Angel of Darkness this had become exaggerated to Jerkass levels.
When Crystal Dynamics reboots the series with Tomb Raider Legend, Lara's personality becomes far more emotional and sensitive. At first, this was something of an improvement. In Tomb Raider: Anniversary, the second Crystal Dynamics game, Lara takes just one human life and turns into Lady Macbeth, wangsting a lot of the time.
TouhouFan Fiction does this a lot with the many many characters who, in the games, have only slight hints at personality traits to begin with. Which makes Touhou a unique case where Flanderization, Character Development and Character Establishment are very often one and the same. In fact, many popular characters have personalities that developed before Word of God announced them in official side works, thus often clashing with the official version, which in turn makes for interesting stories when the different sides try to take control of the plot. One of the best examples is Koakuma, who officially is a mischievous little demon who does erants because she has to and loves to play pranks, while the most famous fan variant is a faithful librarian servant who may even have a crush on her summoner Patchouli.
Reimu is officially a little lazy but still a dutiful Miko who uses her insane luck and instinct to solve problems. Fan works often paint her as a Jerkass Sue who would do anything for money because she is just that poor. The other variant is upping her innate sweetness Up to Eleven.
Marisa is a complex character, best friend and strongest rival to Reimu, hard working, level-headed, but a little on the greedy side, especially when it comes to power and loves flirting and bantering. She has enough reasons for all of those too. Her most common fan version is outright kleptomanic, destructive and has a massive lesbian harem.
Alice is a gifted doll-maker, solitairy, polite, but also cold and neutral towards others. In fan works, she is either a hardcore Tsundere mostly towards Marisa, or an even more hardcore yandere, usually towards Marisa. Both sort of works tend to make her a pathetic, unlucky idiot ignored by Marisa for Reimu, as well.
Remilia and– yes– Flandre are intelligent, young (by vampire standards) ladies, if a little childish. Remilia is usually portrayed as extremely childish, arrogant and demanding, while Flandre is either sweet or a Creepy Child with massive streaks of Person of Mass Destruction. Sakuya is a mysterious maid, Lady of War style and keeps her cool in any situation, but often portrayed as obsessed with her mistress and with hidden streaks of blood-thirsty killer. Meiling is a strong and dutiful gate guardian (who takes a brief afternoon nap daily), yet in fan works is always sleeping on the job. Remilia and Flandre are often turned into evil overlords (especially Flandre), Sakuya either becomes solely obsessed with breast size or a serial killer (her cards have a serial killer theme, with one named after Jack the Ripper, and she suggests Chen be put down), and Meiling is a Butt Monkey.
Yuyuko is the Ojou, knowing and well-reserved, acting dumber than she really is, but since Imperishable Night all she ever does is trying to eat, eat and eat, while Youmu, dutiful if a little clueless samurai gardener bodyguard that she is, is either outright at a loss at what to do or so competent she's been offered job contracts by all other factions already.
Byakuren is The Mentor, All-Loving Hero and one of the nicest characters in a series of usually nice if overly bored strong people. In fan works her messianic nature is exaggerated to Incorruptible Pure Pureness or to The Ditz because she spend so long alone. Shou is always losing stuff, while Nazrin is always busy FINDING said stuff.
Cirno actually is the most powerful fairy by Word of God, but despite all fairies being The Ditz by default, she suffers the treatment of beating Ralph Wiggum in most works. Some fan works have rectified this by making her an Idiot Hero but very likable and compassionate, which is ALSO different from her initial canon appearance, where she is a Creepy Child at best and outright malicious at worst.
It's the same for Utsuho, except how she is a Genius Ditz because she knows absolutely everything about nuclear fusion and assorted technology.
Aya is a slightly over-active photographer and tabloit writer, always busy with making stuff (up). In fan works, she is a creepy pervert who takes delight in takes pictures of others in embarrassing poses or simply Panty Shots.
Yuuka is a strange case, because she is often portrayed as a violent maniac who takes delight in torture and violence, but also has a tender side to those she likes. In canon, her violent side was only seen in the PC-98 era, whose canonicity is disputed; in the Windows era, she's only violent towards people who disturb her flowers, being more interested in creeping them out instead of beating them, and mostly got into fights because the heroines keep accusing her of being in the way/causing an incident.
Yukari is a schemer and controls Gensokyo, but is often asleep and is very weird, even by youkai standards, and loves trolling the hell out of Reimu and whoever crosses her path for giggles, while removing threats to whatever upsets the balance in Gensokyo. It's canon, but fanon either turns her into Deadpool or an Evil Overlord.
While Malfurion Stormrage was always one to put aside differences to face a common threat, Cataclysm has made this his sole character trait. He's so focused on stopping Ragnaros that he blatantly ignores the Horde's attacks on Night Elf settlements, infamously going so far as to defend them in the Leyara questline. This would be somewhat justifiable if he were a strictly neutral character, but he's supposed to be the leader of the Night Elves.
Speaking of Garrosh, the playerbase's complete and utter hatred of the guy has lead to Blizzard Flanderizing him from a young hothead who's slowly coming to understand responsibility, to a brutal Evil Overlord who thinks anything less than his own Kor'kron soldiers are worthless and was messing around with powers far beyond the scope of what any mortal should handle.
Jaina Proudmoore is an interesting case of Flanderization from her original personality into a disputable moment of Character Development / Character Derailment which quickly Flanderized her new personality. In Warcraft III, she was a level-headed, though inexperienced leader who sought peace, but wasn't against fighting if she had too, and at least had semblance of a backbone. In Wrath of the Lich King, she became a full-on pacifist who all but bursts into tears the moment any fighting starts. Then in Mist of Pandaria, Garrosh bombs Theramore, utterly destroying it, and sends Jaina over the edge. She goes from a pacifist to one of the Alliance's biggest proponents for the elimination of the Horde, threatening to destroy all of Orgrimmar with her magic and ordering a cull of the Sunreaver Blood Elves from Dalaran the moment she gets a whiff of a hint they might be aiding Garrosh in his plans.
In Marvel Avengers Alliance, the portrayal of Iron Man is a flat-out Flanderization of one of the most notable traits of his movie counterpart, the snark. Even though in the movies and comics Tony Stark tends to be sarcastic, in this game he takes nothing serious, and constantly makes fun of the current situation and even of other characters who are supposed to be his friends, like Captain America, Thor or Hawkeye.