Rokumonsen is the one AC pilot from the Rubicon Liberation Front who doesn't adhere to their finger-based naming scheme. This is because he's an independent mercenary who is only affiliated with them rather than a full member.
Kate Markson stands out among literally everyone else in Rubicon as she goes only by a proper name instead of a call sign of some kind. Armored Core veterans will also note that her naming style evokes Lana Nielsen aka Nine-Ball, with good reason as she's a proxy for ALLMIND.
Every single case in the Ace Attorney series has the word "Turnabout" somewhere in the title... except for case 5 of the first game's remake, "Rise from the Ashes".
Bendy and the Ink Machine/Bendy and the Dark Revival: The members of the Butcher Gang are named Charley, Barley, Carley and Edgar. Averted with their ink incarnations, which are named Piper, Fisher, Striker and Slicer.
The different playable characters in The Binding of Isaac are all named after biblical figures, except for four of the secret characters: ???, The Lost, The Keeper, and The Forgotten. This is most likely because the other characters are Isaac pretending to be different Biblical characters, while the secret characters are Isaac's body and soul after his suicide.
If you consider it part of the series due to being made by the same company with the same director and having very similar gameplay elements, then Bloodborne is this to the "Souls" series of Demon's Souls, Dark Souls and Dark Souls II.
Two odd names in the six levels of Bug- Insectia, Reptilia, Splot, Quaria, Burrubs, and Arachnia.
Chrono Cross: Most people in the Arni village have common Western names such as Serge, Marge, Leena, Miguel. Then there's Serge's father Wazuki AKA Lynx who has a (rare but still realistic) Japanese name, WRITTEN IN KATAKANA. Radius downplays the trope: his name isn't properly realistic in the West, but is Latin, not Japanese.
Cube Colossus: A.M.U-01 Azrael, for the Biblical Angel of Death, instead of something out of Norse Mythology like the other A.M.Us, Heimdall, Valkyrie, Odin, and Loki.
The main protagonists in Daikatana are Hiro, Mikiko, and Superfly.
Digital Devil Saga has a playable cast filled with meaningful and punny names. There's Serph (Surf, as in water, which is related to ice), Heat (fire), Argilla (means "clay"), Gale (wind), Cielo (means "sky")...and then there's Roland, whose name has absolutely nothing to do with lightning. Also a pretty outstanding case of Aerith and Bob. It makes slightly more sense when you remember that everyone in the playable cast except Roland are A.I.s, but then you find out the A.I.s are based on real people that actually had those names when they were alive, making it weirder. Even in this case, Gale's real self is called David Gale, an actual real-life name. In the novel Quantum Devil Saga: Avatar Tuner this trope is subverted: Serph's real self is Shin Minase (Japanese), Heat is Kazuki Homura (German), Argilla's real self is Annabella di Fiori (Italian), Cielo's real self is Cielo Alondra (from Latin America). All of them are real-life names like Roland, even if they are still loosely tied to elements: Minase means "Ageless Water" in Japanese, Fiori (Italian for "flowers") relates to earth, and Cielo means "Sky" in both Italian and Spanish. The Odd Name Out in this case is Kazuki Homura, which would be a German name if it wasn't written in Kanji (a rarity for German names), and which contains the Japanese word for "Flame".
Dragon Quest III has the Fire families of spells. Sure, Fireball / Firebane / Firebolt and Blaze / Blazemore / Blazemost follow a pattern, but Bang / Boom / Explodet? Its name was changed in the remakes to fit with the rest of spell names.
In the Dusty Dunes Desert area of EarthBound (1994), three men in sombreros who are arranged like the reels of a slot machine introduce themselves as big brother Pancho, little brother Pincho, and their friend Tomas Jefferson. They return in the final area of Mother 3.
Endless Sky: One of the bounty missions has you hunting the "Rat Pack", a fleet of Space Pirates whose ships bear the names various vermin: Rat, Ferret, Stoat, Vixen, Weasel, and Cluny as their flagship. There's no justification given for the flagship's name, but it could be in honor of a specific literary rat.
The Brownie Kings from Eternal Daughter: Mixie, Moxy, Pixie, Poxy, and Randolph.
In Fair A. B. Astherton owns cats named Shelley, Dickens, Hugo and Mr. Wiggins.
In Final Fantasy IV: The After Years, there is a band (no, not that Band) of five Eblaneseninja, enough to form a full party in that game. Of these ninja, the first four are named Tsukinowa, Izayoi, Zangetsu, and Gekkou, Japanese terms for phases of the moon. The last is named Edge — Edge, being one of the heroes from the previous game and their king and master. And his real name is "Edward Geraldine."
Mainline Final Fantasy protagonists from Final Fantasy VII onwards are: Cloud, Squall, Zidane, Tidus ("Sun", from Okinawan tida), Vaan ("Wind", from French vent), Lightning, Noctis ("Night", from Latin nox) and Clive. Zidane and Clive (incidentally the only two not designed by Tetsuya Nomura) have names unrelated to the sky and atmospheric phenomena.
The nations of Valisthea in Final Fantasy XVI are Rosaria, Sanbreque, Waloed, Dhalmek and... Iron Kingdom. Justified, as the Iron Kingdom shares its Mothercrystal with Rosaria and doesn't have a Dominant, unlike the other four.
In Finding Martin Martin's house has penguin lawn ornaments named Huey, Dewey, Louie, Stewie and Chuck.
In Fire Emblem: Shadow Dragon & the Blade of Light, Ogma's three axemen are named Saji, Maji, and Barts in the Japanese version and Cord, Bord and Barst in the American version. This is expounded upon in the ending; the two similarly named ones become woodcuters, while the one that sticks out stays with the army.
In the Fire Emblem Fates DLC chapter "Anna on the Run", the enemies are a group of identical-looking bandits named Lloyd, Llewelyn, Llars, Llucas, Llincoln, Llogan, Lleland, Llamar, Llouis, Llyle, Lliam, Lluther, Llester, and... Tom.
In Fire Emblem: Three Houses, the title for part 2 depends on which house you choose at the start of the game. The Odd Name Out is Crimson Flower, for being the only one that fits the theme naming: the route names come from motifs in Japanese traditional art that represent seasons and colors. The Wind is associated with summer and green (Byleth and Rhea, Sothis, Seteth and Flayn), the Flowers are associated with spring and red (Edelgard), the Snow is associated with winter and blue (Dimitri) and the Moon is associated with fall and gold (Claude), but Dimitri's route is "Azure Moon", Claude's route is "Verdant Wind" and Byleth's route AKA the Church route is "Silver Snow", leaving only Edelgard to have the route associated with her color and motif. It gets even odder in the original Japanese version of the names, as it's Edelgard's route that sticks out. The other three routes were translated in a more straightforward manner ((銀雪の章/Ginsetsu no Shō - "Silver Snow Chapter"; 蒼月の章/Sōgetsu no Shō - "Blue Moon Chapter"; and 翠風の章/Suifū no Shō - "Green Wind Chapter"), Crimson Flower is 紅花の章/Kōka no Shō, which means...."Safflower Chapter." While the floral aspect remains, the color theming does not - in fact, real-life safflowers tend to be orange or yellow, with red flowers being almost non-existant. This route name also has symbolism that was Lost in Translation, as Edelgard's route is the alternative route for the Black Eagles, and the player needs to fulfill several requirements to access it. In folklore, safflowers were thought to be useful in attracting and ensnaring a potential lover for the holder - and luring Byleth to Edelgard's side is something she actively tries to do throughout White Clouds.
Five Nights at Freddy's 2 has the redesigned animatronics: Toy Freddy, Toy Bonnie, Toy Chica, and... The Mangle, who, according to Five Nights at Freddy's World, was named Funtime Foxy before they were broken and turned into an attraction.
In Flight Rising, the first ten elemental deities have a [element-related word]+[title] naming pattern: Earthshaker, Flamecaller, Windsinger, Tidelord, Icewarden, Stormcatcher, Lightweaver, Shadowbinder, Gladekeeper, and Plaguebringer. Meanwhile, the Arcane deity (who is also the youngest of the setting's gods) is simply called the Arcanist.
The demonic Knight Templar Parents antagonizing you are known as Daddy Dearest and Mommy Mearest. Then there's their daughter... Girlfriend, which isn't alliterative, rhyming, or designates her position in the family, and better fits with the naming scheme of her boyfriend, "Boyfriend". Fittingly, she's also the only one not shown to do anything evil.
Of the characters included up to Week 7, everyone either goes by a nickname (Skid and Pump, Tankman) or some kind of identifier (Boyfriend, Girlfriend, Daddy Dearest, Mommy Mearest, Senpai, Monster, and Spirit). This leaves out Pico, the only character going by a real name. Counting planned characters, Hank J. Wimbleton is the only character that has a known full name.
Gatling Gears has all the bosses' names start with a "The", except for one. The Vanguard, The Gardener, The Excavator, Shockstorm, The Bouncer, and The Butler.
In Goodbye Volcano High, Fang's name stands out against their family's traditional Arabic names (Naser, Sabah, Saeed, and Amal). This is justified due to "Fang" being their chosen name after transitioning to being nonbinary, and their deadname fits in with their family's names.
In Grand Theft Auto Online, one of Gerald's jobs is to track down and kill a set of Ballas OGs. From first to last, the names of your targets are Big T, Little T, Small F and Terrance.
The mobile game Hopeless Heroes has a Theme Naming with the various Goops, having their names end with -oop (so we have stuff like Boop, Toop, Stoop, Zoop, etc). One of them however is simply named Daniel.
Hyper Light Drifter: Most bosses are named after tarot cards. The bosses of the eastern, northern, and western sectors are the Hermit, the Hierophant, and the Hanged Man, respectively, and the final boss is Judgment. The boss(es) of the southern sector? The Sentients.
The Handsome Men from Killer7, in true Sentai tradition, are all named after the colors they wear (Handsome Red, Handsome Blue, Handsome White Pearl, etc.,) except for Handsome Dead (who's dark red and yellow.)
All Nobodies have names that are anagrams of their human names with "X" added, which in most cases makes them outlandish-sounding (that is if their human names are not already). All except Naminé, whose name not only is not an anagram of her human's name (Kairi) and does not have an X, it is a perfectly normal real life name. Although while it's not an anagram, it is thematically related to Kairi; kai and nami are Japanese for "sea" and "wave", respectively.
While Xion has an X in her name, the other letters are not anagram of her human name. In fact, she doesn't even have a human form, being a replica of a Nobody, which makes her an outcast within the Organization XIII whose members are otherwise all Nobodies. That doesn't stop her name from having a truckload of meanings, including tide (shio in Japanese), Tatarinow's aster (shion in Japanese), and the anagrams for No. i (imaginary number) and No I (no one).
One quest in Kingdom of Loathing involves finding items for four demonic band members: Bognort, Stinkface, Flargwurm and Jim.
Varus is the only member of the Darkin species whose name doesn't have two As in it. This is because he originally wasn't a Darkin, with his status as one being the result of his lore being retroactively rewritten years after his debut. This is something that his fellow Darkin, Aatrox, will lampshade as part of his taunt against Varus.
Aatrox: "Varus". V-A-R-U-S, your name should have an A and then another A, Varus. There was a memo, Varus, there was a memo.
The Legend of Spyro: Three of the four guardians have names directly referencing their associated element — Ignitus is the fire guardian, Volteer is the electricity guardian, and Terrador is the earth guardian. The exception is Cyril the ice guardian, whose name is derived from the Greek word for "masterful" rather than anything ice-related.
The Legend of Zelda: The Wind Waker: The Tingle brothers: Tingle, Ankle, Knuckle, and David Jr. The latter having a different kind of name is justified for not being actually related to Tingle.
The Maid of Fairewell Heights: Jinn and Lords Whitepeach and Blackberry are the demon world's Cat Pile BROTHERS!! But, Jinn isn't named after a food like Lords Whitepeach and Blackberry.
Makai Kingdom: Dark Lord Valvoga consists of three beings: Ophelia, Dryzen, and Mickey. It does not help that Mickey is decidedly camp and constantly bullied by the other two despite technically being in control.
Most of the Mavericks in the Mega Man X series use Animal Theme Naming in the form of "(Element) (Animal)". The few that buck this trend are named after fungi, flowers, and vegetables: Split Mushroom (from Mega Man X4), Axle the Red (a.k.a. Spike Rosered, X5; more on that below), Tornado Tonion (X7), and Optic Sunflower (X8).
This started all the way back in the original Mega Man X game, where there's, among other animals, an octopus, a penguin, an armadillo, and... er, a kuwanger. Boomer Kuwanger (known as Boomerang Kuwanger in Japanese) is technically a stag beetle, but for some reason he retained most of his strange Japanese name in English translations (the other mavericks have similar names in Japanese, like Icy Penguigo, Storm Eagleed and Launcher Octopuld.)
Mega Man X6 is also the only game where the Mavericks retain their exact Japanese names (regardless of how little sense it makes to Western ears, like Infinity Mijinion), while Mega Man X5 breaks the naming tradition altogether and names the Mavericks after members of Guns N' Roses (leading to names like Mattrex, Duff McWhalen, and Grizzly Slash.)
X5 has an odd name out within the odd names out: The Skiver is the only one not named after a Guns N' Roses member. Still not fitting the "ability + species" theme naming of the other games, but still referencing his sky theme.
Things went back to normal with the New Generation Reploids in X8, with the exception of Gravity Antonion.
After the player takes care of the first wave of four bosses in Mega Man Zero 2, they're free to take on the second wave, consisting of the three surviving Guardians — Sage Harpuia, Fairy Leviathan, and Fighting Fefnir — and Burble Hekelot, a normal Mutos Reploid standing in for his boss, the deceased fourth Guardian Hidden Phantom.
Metroid Prime 2: Echoes: The Dark World counterparts of Temple Grounds, Agon Wastes, Torvus Bog, and Sanctuary Fortress are respectively Sky Temple Grounds, Dark Agon Wastes, Dark Torvus Bog, and Ing Hive. The last one has its name because it's where the Ing proliferate the most.
Metroid Prime 3: Corruption: The main planets visited are Norion, Bryyo, Elysia, and Pirate Homeworld. The last one is the only planet without a fully confirmed name (averted in the Japanese version of the game, where it's called Urtraghus; the only hint suggesting this name in the Western versions is the name of an enemy, Urtragian Shriekbat).
In Middle-earth: Shadow of War, most characters have unrealistic names that mean something in Tolkien's conlangs or are Translation Convention for Westron and/or Rohirric. And then there's the protagonist Talion, whose name is Latin for "eye-for-an-eye" note Tolkien used Anglo-Saxon as translation for Rohirric and Old Norse as translation for Khudzul, but never Latin. And the "Blade of Galadriel" DLC takes this up a notch with the Nazgul sisters Riya and Yuka, whose names are actually JAPANESE note Tolkien rarely mentioned Easterlings by name, but the only one he did confirm was named Khamul, a clearly non-Japanese name.
Mighty No. 9: The Mighty Number team consist of Pyrogen, Cryosphere, Dynatron, Seismic, Battalion, Aviator, Brandish, Countershade, and... Beck. According to the backstory, this is because the Mighty Numbers' creator, Dr. White, designed Mighty No. 9 as a Ridiculously Human Robot, and gave him a human name to reflect this.
Mortal Kombat did this once per game, with three palette-swap ninjas:
The original male ninjas: Scorpion, Sub-Zero, and secret character Reptile. Smoke continues the S-theme, but Noob Saibot doesn't really.
The female ninjas: Kitana, Mileena, and secret character Jade.
And the cyber-ninjas in the third game do it twice: Cyrax, Sektor, and Smoke. Note that Cyrax is one of the few times you see the letter C in Mortal Kombat (granted it's a soft C which is usually left alone), so of course in the Ultimate reboot, he has a Heel–Face Turn. Also note that Smoke is monosyllabic, a throwback to the original smoke, and non-science-fictiony. Also, he actually helps Sub-Zero; too bad he gets thrown in the Heel–Face Revolving Door and ultimately teams up with Noob Saibot.
Mother: The protagonists of the first two games in the trilogy are named Ninten, after the company that published the game, and Ness, an anagram for SNES. Lucas is instead named after one of a pair of twins from the novel The Notebook, which fits with his general dissimilarity to the two and the fact that his game is the only one that doesn't take place in America/Eagleland.
Tactics Ogre has the Foriner sisters: Selye, Shelley, Sisteena, and...Olivia.
The series is named after songs by Queen (whom Yasumi Matsuno was a fan of): "Ogre Battle", "March of the Black Queen", "Let Us Cling Together" and "Person of Lordly Caliber". Except for one: "Knight of Lodis".
Oh Shit!: The ghosts are named Joey, Paul, Willy, and Frankie. Paul is the only one whose name doesn't end in an "-ie"-like sound.
Despite the Onimusha series taking place in Japan for the most part, the majority of Genma don't have Japanese names, at all. Some of them are named after characters in Hamlet, such as Fortinbras, Guildenstein, and Marcellus. The second game introduced Genma with peculiar names, like Ginghamphatts, Jujudormah, and Gogandantess. The only Genma in the series with Japanese names were originally human to begin with and are of Japanese descent. One such character is Oda Nobunaga.
Blinky, Pinky, Inky, and Clyde, the ghosts from Pac-Man. Ms. Pac-Man replaced Clyde with Sue and Jr. Pac-Man replaced him with Tim. According to The Other Wiki, in the original Japanese version, one set of names for them (see here) was Akabei (or "赤ベイ", with 赤 meaning "red"), Pinky, Aosuke (or "青助", with 青 meaning "blue"), and Guzuta (or "愚図た", with 愚図 meaning "indecisive person" or "someone who lags behind"). Guzuta is the only one that doesn't refer to a color.
Belladonna is the only properly named character from the Persona series to be related to the Velvet Room and not have a name that somehow ties into Frankenstein. The remainder are Igor, Elizabeth, Margaret (this one's pretty obscure — she's the ship captain's sister in the novel), Theodore (most likely for Theodore Roszak, author of The Memoirs of Elizabeth Frankenstein), Marie (Mary Shelley, author of Frankenstein) Caroline, Justine, and Lavenza. Belladonna still fits the Frankenstein motif as a whole even if her name doesn't, as she's inspired by the Bride of Frankenstein.
Eevee is the only member of its family not to have "eon" in its name.
Tyrogue is the only one of its family to not have "Hitmon" in its name. And among Tyrogue's three evolutions, there's an Odd Name Out within them: Hitmonlee and Hitmonchan are named after Bruce Lee and Jackie Chan respectively, while Hitmontop is named after...spinning tops.
Keldeo is the only member of the Swords of Justice whose name isn't based on a color and doesn't end with -ion.
The Canon Names to most protagonists are mostly average names, but Red from Pokémon Red and Blue and his Distaff Counterpart Leaf are the exceptions. Red technically is an actual name, though it's quite rare, especially in Japan.
Type: Null is the only Pokémon to not even have a real name.
In Puyo Puyo Tetris, O is technically the only member of the S.S. Tetra not to recieve a Dub Name Change, making him the only crew member whose name is still one letter.
The Generic Dudes Gang of Hats from River City Ransom is a group of thugs with rhyming names (Gary, Cary, Terry, Jerry, etc.) Their leader's name? Ralph.
Until Silent Hill: Origins came out, James was, either accidentally or on purpose, the Odd Man Out of the protagonists whose names otherwise began with H. (Harry, Heather, and Henry.)
Sonic the Hedgehog: Most Funny Animal characters have improper nouns for names, such as "Cream", "Sonic", "Silver", "Knuckles", and "Blaze", usually followed by "the [Species]". The obvious odd one out of the Classic characters is Amy Rose, who has a perfectly 'normal' sounding name. Typically only human characters have names like hers (for example, Maria Robotnik). Amy is also one of the few Funny Animal characters with a surname. Tails also counts, as his real name is the punny but otherwise mundane "Miles Prower".
Back To Nature features a family of Lillia, Basil, Popuri... and Rick. Rick's name is the odd-one out because he originally was unrelated to Popuri. In Harvest Moon 64 he was the cousin to Gray and Ann (thus the red hair they all share). Popuri and her parents were originally florists, not chicken farmers, thus the plant-based theme of their names.
The Dolls from Street Fighter are named after the months of the year... except Cammy. Justified since Cammy no longer works for Bison. Furthermore, all the twelve months' names had already been used.
The strategists of the Suikoden series have always been from the Silverberg family (Shu and Apple, at least, are students of Mathiu), but the fifth game gives you Lucretia Merces, a hot Karayan expy of Zhuge Liang, who has no relation to the Silverbergs in any way. The other side's strategists have nothing to do with the family either.
Super Mario Bros. 3 has the Koopalings, named after famous musicians (Morton, Wendy, Iggy, Roy, Lemmy, and Ludwig). The exception is Larry, who (contrary to popular belief) wasn't named for anyone in particular, but was called that because, according to Word of God, he "just looked like a Larry".
Mario Party 5: All boards end with "Dream" in their names, except for Bowser Nightmare. It's justified, because the standard boards are meant to represent healthy, beautiful dreams while Bowser's Nightmare represents fearful ones.
Paper Mario: The Thousand-Year Door has a trio in Glitzville consisting of a Hammer Bro, Boomerang Bro, and Fire Bro who are respectively named Hamma, Bamma, and Flare.
Super Robot WarsOG Saga: Endless Frontier has group of antagonists call Orchestral Army. Their members have German name based on "The Bremen Town Musicians" (Henne - Hen, Ezel - Donkey and Katze - Cat), then we have a Cute Witch call Kyon. Kyon is Greek for Dog (though it's still odd name out for not being German).
Utawarerumono: Most characters in the trilogy have either Japanese or Ainu-derived names. Then there's Jachdwalt, a distinctly German name. While he is from a different country, his country is not suggested to have a different language or naming tradition, and other characters from his country don't have German names either. This discrepancy is never explained nor even commented on.
Yandere Simulator: Most of the club leaders have Punny Names relating to their club (e.g. Occult Club leader Oka Ruto= Japanese Ranguage for "occult"). The exceptions are Amai Odayaka, Kizana Sunobu (both of whom are among Yandere-chan's rivals), and Fureddo Jonezu (Fred Jones, as the Photography Club are expies of Mystery, Inc).
tend to be orange or yellow, with red flowers being almost non-existant. This route name also has symbolism that was Lost in Translation, as Edelgard's route is the alternative route for the Black Eagles, and the player needs to fulfill several requirements to access it. In folklore, safflowers were thought to be useful in attracting and ensnaring a potential lover for the holder - and luring Byleth to Edelgard's side is something she actively tries to do throughout White Clouds.