The Twins get this in Ouran High School Host Club once they realized that Haruhi could differentiate them. Kaoru becomes the more mature of the two, but is overly self sacrificing. By the time the mini arc is over, they're beginning to force themselves to grow apart by dying their hair and nearly drop the twincest act, but decide that is too much.
The twins, Homare and Misao in Okane Ga Nai. There is no way to distinguish them from one another by appearance, but over the course of the series Homare is shown to be much more emotional, and eventually he realizes he is wildly in love with Ayase.
Gundam 00 featured a replacement twin who at first appears a lot like his murdered twin older brother. This lasts about three episodes when he starts to get pissed by it and shows some people he is very different. In the end, they are not 'that' different... they have similar core personalities, but simply handle life differently starting from there. Remarked when the surviving twin kills the Blood Knight who murdered his entire family, and who his brother died trying to get revenge against - yet doesn't do it out of revenge, but because the other rejected the Last-Second Chance he gave him. Well, that and the guy was about to shoot him.
However, outside of pilotting the same Gundam set, they had slightly different inclinations. Neal was pretty much "The Sniper" of the team and would only resort to full frontal combat in dire situations. On the other hand, Lyle was more well rounded and while he was a skilled sniper as well, he usually would eschew the rifle in the favor of his handguns. You can see this better when the third gundam, which is tailored closer to his own abilities puts more emphasis on multi-targeting over outright sniping.
And then there's Gundam SEED Astray, where the titular Astray Frames start out as palette swaps of each other until they end up in the hands of three different pilots : hot-blooded mechanic Lowe gives his Red Frame a silly loadout of melee weapons such as katanas and a makeshift Shining Finger, cool mercenary Gai outfits the Blue Frame with a large arsenal of guns and artillery, and Big Bad Rondo customizes the Gold Frame using parts scavenged from the recently destroyed Blitz Gundam, granting it stealth and pilebunkers.
The Big Five in Yu-Gi-Oh!. Initially they're an Omniscient Council of Vagueness, with the collective goal of taking over KaibaCorp for unspecified, but undoubtedly sinister intentions. In the "Virtual Nightmare" arc, they're all given separate personalities, and objectives, and while they all share the goal of defeating Kaiba and escaping into the real world, their reasons for hating him are fleshed out, with them being gaining separate backstories and motivations. Big Bad Ganzley and Amoral AttorneyJohnson are just greedy, the rather pitiable Crump is furious at Kaiba for mocking his penguin obsession, Nesbitt's angry about his work being disposed of and his lab destroyed, and Lector's The Resenter par excellence and believes that he should have inherited the company.
Played straight and also zig-zagged in Battle Angel Alita Last Order. Sechs, Elf, and Zwolf start as clones of Alita/Gally in the Tuned arc of the first series, but by the time they are reunited at the start of Last Order, Elf and Zwolf have switched to more waifish bodies and Sechs has gone feral. Sechs's divergence continues when she switches to a male body, while Elf and Zwolf's similarity to Alita actually increases over time.
In Eyeshield 21 Jumonji, Kuroki, and Togano started out as stereotypical delinquents. This didn't last, with Togano becoming an aspiring artist, Jumonji outed as a smart guy hanging out with the wrong crowd, and Kuroki remaning a typical, but friendlier, thug.
Justice League of America: Originally, all of the characters came from self contained comic books and in their individual books they all played The Hero archetype to their own supporting casts. When these characters were pulled together into the Justice League, the result was that the cast was composed of the exact same character type and had the same personality. Over time, their character traits became more diversified and today, the character differences are exaggerated in the team up book and downplayed in each character's solo comics. Superman became more of a boy scout, Batman became more of a jerkass, Green Lantern became more of a jock, and The Flash became more impulsive.
Justice Society of America: Even though the Justice Society came first and the Justice League of America was just a Silver Age update of the Justice Society, because the Justice League was more popular, it was decided that the Justice Society needed to find a new core concept to differentiate it from the Justice League. Several different ideas were tried such as being an Alternate Universe equivalent to the Justice League, being a group of middle-aged superheroes, being a group of senior citizen superheroes, until finally, they found a concept that worked sales-wise, a multigeneration family of superheroes training the next generation.
Guy Gardner started out somewhat more generic when he was first introduced as the other guy the ring could have gone to but was developed into a Jerkass when he became a regular (and more recently, a Jerk with a Heart of Gold). Johns went to even further lengths to distinguish the various Lanterns, when he brought back Hal Jordan and the Corps, by showing how the personalities of the Lanterns affected how they used (or didn't use) their rings and what sort of constructs they built.
Case in point, Rebirth goes into detail about the way Rayner, Gardner, Stewart, Jordan, and Kilowog use their rings. Stewart, being an architect, has constructs that look like a blue print, with every individual detail within them planned out. Rayner, being an artist, often uses a construct pencil to "draw" other constructs, and the eraser construct to change details about them. Gardner's ring is literally leaking green light at all times, because "his willpower can't wait to escape". Jordan likes to go for a combination of brute force and precision, hence boxing gloves, missiles, etc. Kilowog's is the only ring among the regularly appearing characters that makes a sound, and it sounds like a cannon.
Transformers: Skywarp and Thundercracker spent a lot of time as just characters meant to fill space and be pallet swaps for Starscream. Their bios only giving them character. The IDW comics start with them just being two minions, Thundercracker slightly smarter. In Transformers: All Hail Megatron they divide up, Thundercracker abandoning the cause, and Skywarp being more solidly devoted to it. Come TheTransformersIDW Thundercracker has pulled a Heel-Face Turn and helps the Autobots, while Skywarp tries to prove his worth as the Big Bad of Bumblebee's mini-series.
Shazam started out as "Captain Marvel", a Superman knock-off, but eventually DC Comics bought the rights to him. Since both heroes now inhabit the same continuity, the differences are played up; Shazam's powers are magical in nature, which makes him an asset where Superman is weak to magic; and while Superman is "the Big Blue Boy Scout" Shazam is even more so, being a pure-hearted boyin an adult's body.
Rare inverted example; In Cruel Intentions, both Kathryn and Sebastian were attractive, intelligent young people who pride themselves on their ability to bed any member of the opposite sex they choose. The two main differences between them are their sex organs and the expectations society has of them due to said organs. In the prequel Cruel Intentions 2, Sebastian is kind and considerate, and Kathryn is cold, calculating, and uses sex as a weapon; and frequently destroys other peoples lives for her own amusement or revenge. Both try to convert the other to their way of thinking, but Sebastian is broken by Kathryn and ends up becoming a male version of her.
In The Hunger Games Katniss' prep team starts off as basically one character. But through Catching Fire and Mockingjay, Octavia is more emotionally unstable, and Venia is slightly more level headed than the other two.
Originally, The Hardy Boys were fairly interchangeable from each other. Right around the time the series switched publishers in the 1970s, however, they decided to split the characters apart, making Frank much more bookish, shy, and logical, and Joe more athletic, boisterous, and impulsive.
Live Action TV
Starting late in the first season of Maverick, episodes started to alternate between focusing on series mainstay Bret Maverick (played by James Garner) and his brother, Bart (played by Jack Kelly). Although Bret and Bart were written identically (writers were told to always write for Garner, and the producers would later just select which character would lead due to scheduling), the actors' portrayals quickly established Bret as the fun-loving, wisecracking brother, and Bart as the more serious-minded of the two. The same process happened to a later Maverick as well, as Roger Moore played Beau Maverick as a refined gentleman, at odds with the other two brothers' portrayals, despite the character, again, being written exactly the same. As for the final Maverick brother (Robert Colbert as Brent Maverick), he only appeared in two episodes, and thus never really found a personality of his own.
The Cylons of Battlestar Galactica started out mass-produced, with each model line sharing an identical personality. By the end of the series, the models most sympathetic to humans (especially the Sixes and Eights) have diverged to having unique identities and even names for the Sixes. While the antagonistic models such as the Cavils, Dorals, and Simons remained monolithic and identical.
On Stargate Atlantis, the Wraith started off being interchangeable, down to all the male ones being played by James Lafazanos and all the female ones being played by Andee Frizzell. The only exceptions were when more than one Wraith was on-screen at a time. Eventually, Friendly Enemy "Todd" (Christopher Heyerdahl) and Jerkass Woobie "Michael" (Connor Trinneer) came out of the literally nameless mass.
In early episodes of 30 Rock, Grizz and Dot Com were pretty much just a pair of dim-witted bulkheads who follow Tracy around. Now Grizz is an emotional soul and Dot Com is a well-spoken Smart Guy. Their initial lack of characterisation can be put down to no-one ever paying attention to them, which remains a Running Gag.
Brittany and Santana on Glee start out as Quinn's interchangeable minions (Brittany in particular had next to no lines and was basically a prop), with the occasional throwaway line about them secretly having sex. Over the course of the series however, the two gained distinctive personalities of their own: Brittany a Brainless Beauty but a Lovable Alpha Bitch, openly bisexual, and one of the two best dancers in the Glee club; and Santana became one of the best singers in the group, as well as a Spicy Latina and Lipstick Lesbian whose gayngst was perhaps the most beloved storyline of the third season. And their relationship went from a minor running gag to being fully explored. After Finn's death, they became the show's Beta Couple behind Kurt and Blaine.
In The Big Bang Theory, Amy was introduced as a Distaff Counterpart to Sheldon, more or less exactly like him in every way. As the show progressed Amy began to spend time with Penny, became her "Bestie", and began to open up socially, revealing a lonely and troubled childhood responsible for how she is, and developing normal desires for attention and romance from Sheldon that eventually lead to him declaring them an Official Couple.
At the beginning of The O.C. Summer and Holly were distingushable only by hair colour, both being vapid, self absorbed party girls who happened to be friends of Marissa. Summer grew more likeable, became a main character and hooked up with Seth. Holly had an affair with Marissa's boyfriend and was quickly Put on a Bus after the cheating was revealed. This is actually Lampshaded by the show in the "The Chrismukk-huh?" where see an alternate universe where Summer continued to be friends with Holly rather than going through Character Development. It is not a pretty picture.
In Agents of S.H.I.E.L.D., Fitz and Simmons were originally treated as near-identical quirky lab techs - in fact, in the premiere they were first referred to as "Fitzsimmons" and it was only later clarified to the audience that they were in fact two people. Their only major differences were gender and specialty; Fitz is male and the tech expert, Simmons is female and a biologist. Over the course of the first season more differences crop up; with Fitz being a Cowardly Lion and having a crush on Simmons but not being able to say so, while Simmons is a bit of a Nightmare Fetishist but a horrible liar. And Fitz may have suffered brain damage in the season finale, which could differentiate them even more.
In Noob, Couette started out as Sparadrap's Distaff Counterpart before she started showing signs of being more self-centered than him (e.g. sometime complaning about the state of her clothes in the middle of a battle) and knowing random pieces of in-game trivia. In the meantime, Sparadrap remained the franchise poster boy for Kindhearted Simpleton. The divergent evolution is at different stages depending on the media between Couette being a frequent no-show in the webseries, the novels covering short timespans with much bigger time skips between them and the comic storyline being less advanced than the two previous.
In the Over the Hedge comic, Verne used to be a lot more like RJ; you could usually swap their dialog with neither one seeming out of character. Then the cartoonists decided they needed more conflict. Today, Verne has so little in common with RJ that we wonder why Verne doesn't leave. (He does sometimes, but never for long.)
If two people debut as a tag team they'll start very similar to each other, but once they break apart they start developing their own personalities and move sets, see Shawn Michaels and the Marty Jannetty, Matt Hardy and Jeff Hardy and Edge and Christian. Usually doesn't happen in the case of identical twins, though.
Inverted in the case of twins Dave and highly prolific referee Earl Hebner. Dave Hebner was the assigned official for an explosive 1988 rematch of the legendary Hulk Hogan vs. André the Giant title match from the previous year's WrestleMania III. But unbeknownst to Hogan, André's manager Ted DiBiase had bribed an unknown to get plastic surgery to look like Hebner (in the unknown's role was Earl Hebner. Earl and Dave are identical twins, so this was easy to pull off). In Dave's place in the ring (while Dave was locked in a closet backstage), Earl played the Evil Twin, counting a clearly invalid pinfall against Hogan. Although the twin referee angle was thoroughly explored in WWF Magazine, it was very quickly dropped though due to Dave suffering an injury. Earl would later become a normal "good guy" referee like his brother.
Luigi from the Super Mario Bros. series, the former Trope Namer and current God of the Trope, was originally a Palette Swap of his brother Mario, and was identical to him in every way. He has since been given his own high-jumping, low-traction style of gameplay, as well as a taller and more slender character design. His personality has drifted off as well; Mario is still portrayed as simply heroic and courageous, but Luigi has developed a second-banana complex, has become somewhat cowardly (especially regarding ghosts), and harbors dark secrets and Hidden Depths. Some fans prefer Luigi to the squeaky-clean Mario for this reason.
Daisy was nearly a palette swap of Peach, with the only exception being that her skin was slightly dark while Peach was fair skinned. By Mario Party 4 and later, Daisy's skin became fair like Peach's, but Daisy's hair was shortened to neck length, gotten a different hairstyle, and her eyes were made larger in comparison to Peach's eyes.
Another example from the Mario series is the Koopalings Lemmy and Iggy. While the two looked rather◊ similar◊ in earlier games, Iggy's appearance in New Super Mario Bros. Wii has him looking... well, like this◊. It's also notable that Iggy seems to have apparently gone insane... Well, more insane...
In Super Smash Bros. Brawl, the characters that were clones in Melee got more of this to the point that there are no true clones in Brawl; there are only semi-clones.
This trope's original name, "Luigification," came from Smash Bros. fandom, referring to Luigi becoming less of a Mario clone between the original Super Smash Bros. and Melee. Naming it after Luigi was very fitting even ignoring Smash Bros., as noted above.
Ryu and Ken originally played the exact same way in Street Fighter I. They have since been differentiated in both moveset and characterization. Although they are both use the same fighting style, Ryu is now a Hadoken specialist and usually fights defensively, while Ken is more aggressive and prefers the Shoryuken.
Street Fighter III introduced twin brothers Yun and Yang. Originally, they played identically (to the point that they shared the same slot in the player select screen; you'd select Yang with a kick button), but in 2nd Impact, Yun and Yang were officially made into separate characters with different Special Moves and Super Arts.
Most of the clones in Soulcalibur III also received this. Siegfried and Nightmare had their movesets almost entirely differentiated after being nearly identical in the first game and different costumes for the same character in the second.
Soulcalibur IV does this to Amy, who in SCIII had the generic create-a-character Rapier moveset.
The differentiation was actually made in a later arcade version of SCIII in which they decided to shift Amy, Li Long and Hwang Seong-gyeong into more intricate arcade-worthy characters. It's also actually more of an inversion, because the create-a-character classes were different enough from the originals for them to be missed in Soulcalibur IV's create-a-modes. Many fans of III were pissed that their characters had to fight the exact same way as the main cast.
It should be noted that Li Long and Hwang have reverse examples as their appearances in Soulcalibur IV and Broken Destiny's Quick Match mode have them use the same moves as their replacements Maxi and Yun-seong respectively.
Orcs and Humans were pretty identical in the first two Warcraft games, but in Warcraft III, humans are the Jack of All Stats while orcs have powerful but expensive units and weak magic.
In Warcraft II, the two races were identical in every aspect, except their respective Magic Knights (Paladin and Ogre-mage) and true mages (Mage and Death Knight) had different spells. The Orcs had most of the advantage with Bloodlust over Healing, but Mages had some tricks up their sleeve in the late-game with Invisibility and Polymorph.
Also, in World of Warcraft, the Shaman and the Paladin class both inverted and played this straight. The Shaman was originally Horde-only, just as the Paladin was Alliance exclusive. While both classes are Magic Knights, the problem was that they functioned in entirely different manners and it turned out to be a pain to balance out. They tried several things, including making the two classes more and more similar. This was not really liked (particularly as the classes have very different functions outside of buffing), and the first expansion gave both factions access to them, the Alliance gaining Draenei shamans and the Horde getting Blood Elf paladins. They were then free to start their divergent evolution without worrying about wrecking the faction power balance.
In the Star Fox series, all of Fox's wingmen were pretty much the same at the beginning, other than in personality. This was changed in the unreleased Star Fox 2, which allowed you to choose your character, with each flying a different ship with different properties. It reverted back in Star Fox 64, where you could only play as characters other than Fox in multiplayer, and that being a purely cosmetic choice. Things stayed that way until Star Fox Command which finally incorporated the different ships choices from Star Fox 2.
In Sonic the Hedgehog 2, Sonic and Tails played the same way. Starting with Sonic the Hedgehog 3, Tails was given his own play style. (He is unable to use the shield power-ups as double jumps, but gains a limited flying ability.)
Tails' play style has gotten to the point of being unrecognizable in some of the more recent games, most memorably walking in a mecha in Sonic Adventure 2.
Also, Shadow in Sonic the Hedgehog (2006). His techniques went from being very similar to Sonic in Sonic Adventure 2 and Sonic Heroes to a different style. However, the fact that he became slower could raise different questions.
Inverted in the F-Zero series. The series originally featured four characters with markedly different play styles, but as the cast expanded to include Loads and Loads of Characters, those original four have drifted to the middle, becoming little more than mildly differentiated Jacks of All Stats.
In The King of Fighters, Kyo and Iori, like Ryu and Ken, were essentially clones of each other in their original appearance, but their gameplay styles began to diverge as times went by: Kyo lost his fireball and gained more powerful normal moves while Iori became quicker and more mobile.
And then, by The King of Fighters XII, Iori had lost his fire powers completely, while Kyo pretty much lost his fiery "Rekka-style" moves and had regained his fireball... (Though in XIII, the Rekka-style Kyo and Flames Iori are available as DLC alongside the more "classic" Kyo and the flameless Iori.)
Even more so, Clark and Ralf from the same series (working for an actual honest-to-gosh Colonel Badass, Heidern) start as nearly identical wrestler/brawler characters, but over the years have differentiated so that Ralf has more punching-based "brawling" special moves and fewer and less-effective command throws (although still more than the average character) and Clark has become almost a pure wrestler, with more throws and almost no other special moves. At the same time, their personalities were distinguished, with Clark being the quiet, sensitive, friendly guy and Ralf being quite the Boisterous Bruiser. They are both still complete badasses, of course, and compared to the rest of the cast, effectively Badass Normals.
Ryo Sakazaki and his best buddy Robert Garcia, the Ryu and Ken analogues of Art of Fighting, have this as part of their backstory. Ryo's principle of Kyokugen Karate, while well-balanced, seems to have a slight emphasis on punching and striking techniques, whereas Robert's style focuses on kicks. Note that this difference was established well before Ken would start incorporating a larger repertoire of kicks into his moveset in later iterations of Street Fighter.
In Super Robot Wars Alpha, the player built up their own character by selecting genders, choosing a face (from four males and four females), giving them names, and adding a personality (Cool, Shy, Weird, or Hot-Blooded) and accompanying voice. The Super Robot Wars Original Generation sub-series combined these factors and fleshed them out into the characters Kusuha Mizuha, Brooklyn "Bullet" Luckfield, Rio Mei Long, Ryoto Hikawa, Leona Garstein, Tasuku Shinguji, Yuuki Jaggar, and Ricarla "Carla" Borgnine (which were the default names associated with each character archetype/gender combination).
Alpha 2 and 3 then adopted the Kusuha and Bullet characters as the canon heroes of Alpha (with the "player" and main character assumed to have been Kusuha) and developed them even further, taking their story and character development to appropriate extremes.
It's worth noting that Super Robot Wars 4 did this, as well. However, only two of the eight "standard" characters (those being Irmgult "Irm" Kazahara and Ring Mao) have been included in Original Generation at this time. As a Mythology Gag, in OG (and their cameos in Alpha) they're significantly older than they were in the games they first appeared in, and instead of being a standard couple as per 4 and its re-releases, they bicker Like an Old Married Couple.
Metal Slug is a very well known case of progressive Divergent Character Evolution. In the first game, Tarma is basically just a Palette Swap of Marco, who even had the same death scream as him. In 2, although Fio is not an exact Palette Swap of Eri, she also has the same death scream as her. In X and 3, every character had a different death scream at last, and was given some backstory. And finally, in 6, they were completely differentiated by being given different in-game abilities.
Virtua Fighter's Sarah and Jacky Bryant have very similar fighting styles at first. Throughout the sequels however, they have developed far different fighting styles and backstories over the course of five games. Sarah's official fighting style has been changed from Jeet Kune Do to just Martial Arts (or more specifically, what the Japanese definition of the English term "Martial Arts").
In a very odd bit of differentiation mixup, the Dead or Alive series features the extended ninja sub-plot playing itself out in the characters' fighting styles as well. Kasumi and Ayane, the game's Bash Brothers pair, are similar in fighting style, though with differences: Kasumi's moves set up follow-up combos far more easily, while Ayane is greased lightning with lots of very fast but proportionately weaker strikes. Hayabusa, Kasumi's bodyguard and friend, shares some of her moves, but is slightly more powerful than either for sheer hit potential and has more grappling techniques. Hayate, Kasumi's brother, first appeared in Dead or Alive 2 as Ein, an amnesiac, featuring a similar fighting style to Kasumi, but with much more emphasis on punishing single hits and short combos, though he kept some of the acrobatics. Then Dead or Alive 3 introduced Hitomi, his training partner during his amnesiac phase who is a pure karate practitioner as opposed to Hayate's karate/ninjutsu hybrid, and is slightly harder hitting and faster than him, but much more linear, lacking Hayate's jumping abilities.
Definitively Leon and Bayman. Bayman was in the first Dead or Alive, but was replaced by Leon in Dead or Alive 2. They retained their similarities in Dead or Alive 3, where they both appeared, but in Dead or Alive 4, Bayman has gained a bit more speed to his moves, while Leon retains a more powerful strike potential, and Spartan Nicole-458 uses their shared Russian Sabo style as a skeleton upon which the rest of her unique style was built up from.
This is fairly common in Dead or Alive, as much research was put into replicating the fighting styles of the individual characters from real life martial arts. As such, fighting arts with common roots often show it quite well.
Super Double Dragon differentiated Billy's and Jimmy's fighting styles by giving them different basic moves, giving Billy the faster attacks and Jimmy the stronger ones. No other Double Dragon game attempted to give the Lee brothers different moves besides the iPhone version and the two fighting games.
The all-girl fighting series Variable Geo has done this exactly twice. Initially, Yuka and Chiho played very similarly to one another, with the only real difference between them being their differently animated special moves. However, as the series went on, Chiho developed into more of a Glass Cannon by playing up her ninja-ness and giving her new abilities while Yuka remained largely the same balanced character. When Yuka was sidelined for a later game's story mode, she was replaced with Tamao, an AscendedHero-Worshipper who copied all of Yuka's moves. The following game had them diverge by once again keeping Yuka more or less the same, while turning Tamao into a borderline Joke Character who botched her attacks and had to improvise on the fly to stay in the game.
In early versions of Akatsuki Blitzkampf, Adler was a palette swap of Elektrosoldat, but when he was turned into his own character his moves got radically different inputs and properties. Similarly, in the arcade version Perfecti is no longer a palette swap of Mycale - she is instead an entirely different character with no shared moves.
The first Twisted Metal's character roster contained a dune buggy called Pit Viper which spat out acid blobs as a special attack. However, when the time came for the sequel, instead of repeating the same move (projectiles were extremely common as it stood), they gave it a new one (a jump-based slamming attack) to differentiate it more from other vehicles, and they also redid its color scheme, calling the vehicle Grasshopper from then on.
In what may be a shocking discovery for recent Fire Emblem fans, in thefirst game the Fragile Speedster Pegasus Knights promoted into the Mighty Glacier Dragon/Wyvern Rider class, making the latter simply an upgrade of the former (and just as dodgy). Eventually Genealogy of Holy War put an end to this madness by making them different classes, albeit the previous game started this process by giving Pegasi a decent Resistancetekken (Magic Defense) stat that they lost when promoting (this also applies to the remake of the first game).
The Mortal Kombat series was infamous for having several Palette Swap characters. It started with Scorpion and Sub Zero—same sprite, same basic moves, different special moves, different standing animations. Then they added Reptile as a hidden boss—the same sprite, only green, and with both Sub-Zero's and Scorpion's special moves. Several sequels and home versions later, there were eight palette swapped male ninjas, four palette swapped female ninjas, and three palette swapped cyborg ninjas. Once the games became 3D, all characters were each given a unique model and, since they were no longer sharing the same digitized sprites, they could have different basic moves.
Done with several boss characters in Tekken, e.g. Kunimitsu was initially a gender-neutralPalette Swap of Yoshimitsu, but in the second game was clearly modeled as female and given a slightly different moveset. The first Tekken Tag Tournament uses her Tekken 2 persona and moves with a few additional touches, but in Tekken Tag Tournament 2 she was given a brand new move set that differentiates her from Yoshimitsu.
Jin started as a Suspiciously Similar Substitute for his father Kazuya, but with a few moves from his mother Jun (who was also absent). Jin got his own fighting style when Kazuya came back in 4.
Anna started out as what amounted to an alternative costume for her sister Nina. Nowadays Anna has an almost entirely different moveset, and some of the moves she still shares with Nina have been given a personal twist. Notably, she was only included in Tekken 3 at the last minute, whereas other clone characters weren't, which meant they significantly changed her moves from that point on.
In the first two games Lee was a clone of Marshall Law with the occasional special move. From Tekken Tag Tournament onward, he grew to be a more distinctive character with better combos.
Jack and P-Jack had the same moves in the first Tekken game, although P-Jack was more powerful and looked cooler. In the second, P-Jack can fly whereas Jack-2 can't. This was carried over to Gun Jack and all the Jacks afterwards, as well as being retroactively applied to Jack-2 when he appeared in Tekken Tag Tournament.
In the first game, Jack, P. Jack, Kuma and Ganryu used almost entirely the same moveset. This was expanded slightly in Tekken 2, giving them individual special moves, but they still had a lot of the core moves. P. Jack notably introduced his flight ability. Tekken 3 sought to resolve the similarities by getting rid of clone characters, so it removed Ganryu, only included one Jack (Gun Jack) who had P. Jack's introduced moves, and introduced Kuma's son, who can't hit as hard as the original Kuma and has some comedy special moves, as well as his clone, Panda. Ganryu was absent from Tekken 4 as well but had an updated moveset when he returned in Tekken 5. Also in Tekken 5, Kuma and Ganryu were both given different punch moves to differentiate them from Jack-5. By Tekken Tag Tournament 2 you can play as all four and they are all sufficiently different.
In Tekken 4, Miharu Hirano once shared the moveset of her friend Ling Xiayou. It's not until Tekken Tag Tournament 2 where she finally becomes her own character and different moveset variations. Not to mention that she got Progressively Prettier.
Metal Gear Solid 2's Raiden starts out playing identically to Snake. It isn't until the very end of the game that he gets the sword that allows him to showcase his Implausible Fencing Powers, which Snake doesn't possess. His switch from being a gameplay clone of Snake to having his own play style is actually part of the plot.
Mega Man X3 gave Zero his first playable appearance, where he played like X but with a Beam Saber upgrade (which X can later in the game). In the next game, Zero traded his Z Buster style for a purely close range style to completely distance himself from his partner.
X7, with Axl's debut appearance. Aside from his Copy, dodge, hovering and a couple of different guns, Axl was very similar to X in style and how he used enemy weapons. X8 modified Axl's play style: he retained his Copy, dodge and hover moves, while getting the unique ability to aim his gun in the eight cardinal directions (though he had to stand/hover in one place while firing, unlike X). For each boss defeated, he instead received a new gun that fired projectiles based on a secondary attack each boss used, with different looks and properties from X's, and without needing weapon energy to boot.
Sonic Generations has a variation involving stages. Seaside Hill was originally a complete throwback to Green Hill Zone, having palm trees and checkered soil, but since Green Hill Zone has reappeared playing up those elements, Seaside Hill in Generations plays up the ruins and water aspect more and even adding underwater elements.
Happens in the Sengoku Basara series with Matsu and Kasuga. Both formerly used Kenshin and Sasuke's movesets before gaining their own in the second game. Similarly, a few NPCs who used polearms merely had copies of either Toshie or Shingen's movesets before actually getting their own.
In Rhythm Heaven for the GBA, the Space Dancers and Cosmo Dancers were interchangeable, the Cosmo Dancers only representing a higher difficulty level. In the DS version, both sets of dancers received minor redesigns and hobbies, with the Space Dancers being the focus of the Rhythm Rally games and the Cosmo Dancers being the focus of the Space Soccer games.
The original Parodius for the MSX gave its characters different personalities, but they all used the Gradius moveset. Parodius Da! did give Vic Viper, Octopus, Twinbee and Pentarou each a different moveset.
When Marvel vs. Capcom 2: New Age Of Heroes came out, this trope came into play with Iron Man and War Machine (who debuted in the first game as a palette swap of the former). Originally, War Machine would fire lasers for some of his moves (Shoulder Cannon, Proton Cannon) in a similar manner as Iron Man (never mind that WM's laser came from his shoulder as opposed to IM's chest) and had one more Hyper Combo (War Destroyer) than him. By the time the second game came out, War Machine fired missiles instead while Iron Man retained the lasers.
In Battletoads and Battletoads and Double Dragon, the toads all played the same, and while large sprites and artwork gave them individual designs, their in-game sprites were just recolors. Battletoads in Battlemaniacs gave them different combos and finishing moves (though they still functioned the same) and their sprites now reflected the different designs from the artwork. The arcade game took this even further with by making Rash a Fragile Speedster, Zitz a Jack of All Stats, and Pimple a Mighty Glacier, all with their own moves.
Similarly initially all the toads used the same transformations, mostly blunt objets like ram horns, boots, and wrecking balls. Battlemaniacs gave them individual themes, with Rash prefering razor sharp weapons like axes and claws, while Pimple took the bludgeoning techniques Up to Eleven using anvils and stone fists. When the arcade game came in, Zitz used his greater intellect to create technology like bulldozers and power drills.
In the original Valkyrie Profile, Lenneth was the only playable valkyrie, so there was no need to set her apart from her sisters. She could use swords and bows in battle. Hrist appears as an enemy in the game as well, but she's just a Palette Swap of Lenneth, with black armor and hair and a red Nibelung Valesti. In the second game, all three valkyries are playable. Lenneth loses her ability to use bows, and they become the weapon of choice for Silmeria. Hrist uses spears in battle, a weapon that Lenneth couldn't use at all in the first game. All three sisters use swords for Nibelung Valesti, though.
The Materials of the Magical Girl Lyrical Nanoha A's Portable games. When they were originally introduced as a trio of Evil Twins in The Battle of Aces, they were basically Palette Swaps of the three Aces except with different stats. When they returned in The Gears of Destiny sequel due to popular demand, they received their own unique move sets to differentiate them from their originals. This gets several Lampshade Hangings in sequel and the supplementary materials related to it, such as the Materials explaining that the time they spent recovering from their deaths was used to devise their own fighting styles and spells, and other characters pointing out that for copies, they don't actually act, fight, or even look that much like the people they were supposed to be based on.
Zigzagged throughout the Disgaea series. In the first first game, many of the basic creatable classes have male-female variation, which except for sprites and tiny Stat variations, are exactly the same. In the second game, each class is given different unique passive abilities to differentiate them, and there are more variations to the Stat spread of the male-female variants (like how the Male Warrior has better HP and DEF and is better at Axe while the Female Warrior has more HIT and SPD and better with Spears). The third game, however introduces more male-female variants to the existing single-gender classes (for example now there's a male version of the previously female-only Archers), with differing Evilities and secondary weapon (the male archer can also learn Sword skills while the female can learn Spear skills), but nearly identical Stats. The fourth game then removes nearly all gender variants introduced in the third game.
In Pac Man Party, the four iconic ghosts of Pac-Man were given more distinctive looks in order to differentiate one another. No longer were they simple Palette Swaps of one another. Each of the ghosts had distinctive "hairstyles". Blinky retained the basic ghost shape, Inky was made skinnier, Pinky was given more feminine features, and Clyde became fat and huge.
In Higurashi no Naku Koro ni Matsuri Oka, Hanyuu's daughter, looked exactly like Rika except her hair was darker. In Kotohogushi-hen in Kizuna for the Nintendo DS she got a new sprite.
"Soap" MacTavish was the typical silent protagonist for Call of Duty: Modern Warfare, but in Modern Warfare 2 and 3, he was made into a non-player character for several missions, and accordingly given a strong personality and voice actor.
In Super Smash Bros. Brawl, Pit has a palette swap which gave him black hair and black wings. But differs in appearance only. In Kid Icarus: Uprising they took that palette swap and turned him into the anti-hero Dark Pit, with a entirely different personality and having layers of depth.
Punch-Out!! has a fair few characters that have evolved over the years, the most notable being Aran Ryan. In the SNES game, he was a bland palette swap of Pizza Pasta who fought by the rules. In the Wii game, he's a complete lunatic who threatens Mac, the referee and the audience and breaks just about every rule of boxing, from using his elbows to loading his gloves with horseshoes to tying a rope to one of said horseshoe gloves and using it as a goddamn flail.
Pokémon Gold and Silver have four executives of Team Rocket, who are all unnamed and (aside from the one woman) identical in appearance. The remakes, HeartGold and SoulSilver, flesh out their characters, giving each a unique name and design.
Happens to Nick and Shep in Schlock Mercenary. Originally, they were both idiots. Shep gradually got smarter, moving up to about average IQ; Nick...didn't.
Nick also didn't follow the fate of the other beef-chunk recruits either though, he's still with the company (Shep retired and Hob died).
There's 750 millions of Gav's gate-clones. It was kind of fun until everyone used to them, but... Eventually they started "The Diversity Engineering Institute". After all, 750,000,000 borderline mad scientists will obviously do more and better if each have somewhat different perspective.
Occurs with Akuma and Kari in the sprite comic Akuma TH. They both started out as literal Shotoclones, both using the same fighting style. They diverged fairly quickly however, with Akuma focusing on energy attacks and Kari focusing on punches and kicks. Kari did the most deviating, most notably with her signature Monsoon Kick, a hurricane kick that rotates vertically and moves horizontally, instead of the other way around.
Elliot and Ellen started out being almost exactly the same apart from their genders, but that is justified since Ellen is a Opposite-Sex Clone of Elliot and was "born" with a perfect copy of his memories and personality. However, her initial Cloning Blues and subsequent attempts to establish her own identity led to this trope. (Which is alsoillustrated in the same "failed at perversion" comic above.)
Dorm Life: Britney and Courtney started off as seemingly-interchangeable Alpha Bitches, although there were subtle clues from the beginning that Britney was much smarter than Courtney. Once Britney and Mike started bonding, Britney's Hidden Depths came more into play. Since an entire season of Dorm Life would be produced at one time, this was done intentionally.
Ink City has a crack community called Labocabana, the events within being noncanon to the main game. This has resulted in certain characters developing very differently within Labocanon, such as Yakko and Dot. This has had direct effects on the main story, thanks to Labo!Dot crossing the Moral Event Horizon and her mun trying to prevent IC!Dot from making the same choice by showing her what happened through the Fourth Wall.
Zig-zagged by The Nostalgia Chick and The Nostalgia Critic. She started out being just a simple girl version of his basic traits - snarky manchild doing linear reviews – but then something changed. She got a three dimensional characterization of her own, as well as adopting more analysis-review Style, but the similarities ran much deeper (to name but a few; both have histories of abuse, bad inferiority superiority complexes, desperation for power and psychopathic child tendencies) as well as their differences turning ying-yang (overly dominant/worringly submissive, emotionally repressed/can't hide anything, hates kids but loves animals/hates animals but loves kids), much to her self-loathing denial and his clingy love.
The eponymous Venture Bros. were originally written exactly the same - Pollyanna Hardy Boys parodies that were forever trying to solve mysteries. By the end of Season 3, Hank has become the more masculine and adventurous of the two (as well as a bit of a wannabe Casanova) while Dean is sensitive, intelligent and extremely afraid of sex.
Justified as at the end of season 3, all of the brothers' clones are killed in a large battle as a makeshift army of soft zombie-like bodies (It Makes Sense in Context) and now have to live as anyone else does instead of the convenience of death being incredibly cheap for Dr. Venture when you can just roll out more clones and have no personality developments as a result.
Bart and Lisa Simpson started out as a pair of interchangeable brats. Both were shameless pranksters and not too bright, their main function being to drive their parents up the wall. This worked well for the original three-minute Ullman shorts, which didn't have much time for characterization. The first few episodes of the regular series feature this portrayal as well, with Lisa causing as much trouble as Bart. The writers decided having two identical characters wasn't very interesting in a half-hour format, so the episode "Moaning Lisa" was produced, which re-creates Lisa as artistic, sensitive, highly intelligent, and basically the total opposite of her brother. This version of the character has remained ever since.
Note there were some slight differences in the original shorts, where Lisa was a delinquent, but still somewhat wilier and reserved than Bart and usually more a Greek Chorus to his antics (and eventual comeuppance). Her later characterization is more a case of taking a very vague trait and exaggerating it to it's fullest extreme.
Kyle and Stan from South Park used to have pretty much the same personality in earlier seasons. Now they are still very alike, but their interests and attitudes differ. Kyle is smarter and more reactionary, especially when Cartman is around. Stan is more down to earth, often taking the role of the Only SaneEveryman, as well as being a bit more sensitive at times.
In a similar vein to the Simpsons example, Cosmo and Wanda began life as "two halves of an idiot", a pair of cheerful, wacky fairies. By the start of the second season, said traits were absorbed and amplified by Cosmo, while Wanda became more down to earth in order to balance off the couple.
On Teen Titans, Speedy was originally a Robin expy, playing his Foil in his first appearance. He soon became more of a egoistical "Bad Boy." It's even lampshaded in one episode after he saves a child's cat:
Boy: Thanks, Robin! I like your other costume better though.
Speedy: I'm not Robin!
Inverted in Teen Titans Go!. Speedy is more like Robin than ever before. They even have the same body shape and voice. Exploited in-universe, where they swapped clothes and hairstyles and nobody knew the difference.
In their first few appearances, Chip 'n Dale were identical in every way. Later, Dale gained a red nose, buck teeth, and a goofier personality. Chip more or less kept his original looks, but became more of a Straight Man to Dale.
Rico's appearence wise evolved too; in the movie he looks like a taller and skinnier Skipper and you could barely tell him apart from him or Kowalski. But in A Christmas Caper and later the series he has a scar on his beak and three feathers sticking up like hair to help him stand out.
On Invader Zim's first episode, the Almighty Tallests basically take turns between being The Ditz and the Straight Man for each other. By "Backseat Drivers from Beyond the Stars" Red was established as the smarter one while Purple was more emotional and impulsive. (Though they still both spend most of their time yelling at people and stuffing their faces.)
On the Rugrats tenth anniversary documentary the creators noted that this happened to Phil and Lil: Lil became girlier while Phil kept most of the pair's original interest in grossness.
Taken further in the Spin-OffAll Grown Up!, which features one episode where Lil gets annoyed that everyone thinks of them as an identical pair.
In another, they manifest secondary powers: Blossom getting ice breath, Bubbles becoming an Omniglot and Buttercup having to come to terms with merely being a Flying Brick.
In Total Drama Island, Heterosexual Life-Partners Katie and Sadie originally had pretty much the exact same personality—eternally-happy, sweet, innocent girls who couldn't bear parting from each other. Nowadays, Katie has kept the original personality of the two, but Sadie is now slightly more practical and willing to drop her friend during certain situations. This evolution was made especially obvious with Beth and Lindsay, who became the pair's Expies in Total Drama Action.
Frizz and Nug of The Dreamstone started off as two interchangable Cowardly Sidekicks for Sgt Blob. Further on in the first season, Frizz became increasingly cynical and neurotic, while Nug became more dopey and upbeat.
Played straight for the final season, where they start to revert back to original personalities.
As mentioned in the Teenage Mutant Ninja Turtles entry in the above comics section, this has happened with the protagonists, though the 2012 show looks to take it even further by giving the turtles body-types that are plausible given their individual life-styles (Leonardo is able-bodied, Raphael somewhat huskier than the rest, Michelangelo slightly chubbier, and Donatello tall and lanky), that presumably is made to make them more recognizable even without the weapons and bandannas.
Gargoyles: The Pack. Each member had a different personality, but in their debut they all shared the same motive and all were basically just assassins who wanted a good fight. As the series went on, each got Character Development, and episodes away from the others:
Fox was revealed to be a very adept schemer and was manipulating the pack for Xanatos, who she had fallen in love with and married.
Wolf, The Dragon mutated himself into a Wolfman and became The Starscream to the new leader Coyote, later he teamed up with his ancestor, the very man who killed the series gargoyle clan.
Jackal and Hyena were just the Ax-CrazyBrother-Sister Team Hyena developed an attraction to the robot Coyote, and Jackal gained the power over death and attempting genocide on the world.
Dingo, the explosives expert and the most practically minded went on to leave the pack as the others began to get lose their humanity, worked with Fox as a security guard (as their original security guard was in jail), before revealing his dream of being a hero, and teaming up with a Hive Mind robot. Dingo would later be one of the stars of a Spin-Off comic.
Gordon, Henry and James of Thomas the Tank Engine, while having many solo stories, usually acted as a near interchangeable trio of arrogant peers, bickering with other engines or making pompous remarks. As season passed the three began to appear together less and gained more individual characteristics. Henry in particular became far less egotistical, converting into a sensitive Hypochondriac and Nature Lover. James and Gordon retained their vanity as their defining quirks, however while Gordon became the main team's Grumpy Bear, James became more cheerful and mischevious (and by Season Seventeen seems to have become The Prankster). This evolution occurred in The Railway Series novels as well, albeit to a lesser extent due to the show's more evident Flanderization.
Like Pac Man Party from which it bases its character designs on, Pac-Man and the Ghostly Adventures gave the ghost gang distinctive designs. The Pac-Worlders other than Pac-Man and his parents also count as in most iterations, many of them simply looked like Pac-Man but with a few distinguishing physical characteristics and pieces of clothing. Here in this adaptation, not only do all of the Pac-Worlders have various different body shapes but they also vary in color.
Originally Donald Duck's nephews Huey, Dewey and Louie were pretty much identical in both personality and design. Later they were given different colored clothes and by the 90s they had gained distinguishable personalities, made most noticeable in Quack Pack.
In the Rainbow Magic movie, Rachel is quieter and more serious, while Kirsty is outgoing and positive. In the books they're pretty much interchangeable.