Ace Combat 5: The Unsung War featured the other Kei Nagase, the only female in the entire game until the brief late-mission appearance of Bartlett's old flame.
Ace Combat Zero: The Belkan War goes for a Token Enemy Female again and gives us Marcela Vasquez, the only female boss-level ace and the only woman to get her own interview. Also, out of 169 named aces in the game, only 9 are female. That's about 19 to 1 male-to-female ratio.
Ace Combat 6: Fires of Liberation tried to address this issue by showing a part of the story through the eyes of Melissa and Ludmila, two female refugees wandering the war-torn Emmeria, looking for their daughter and fiance, respectively. Also, it had a Token Enemy Female, Irena Dvornik, as well as allied pilot Lanner.
On a more meta level, Janice is so far the only playable female character in a twenty years-old series. And only for half a mission.
Age of Empires later added in female villagers to the series (villagers may be either gender) in response to a lack of women in the first game. Justified otherwise since virtually all other units were combatants, and for most societies their militaries were mostly men (women fought in wars even if they weren't allowed, of course, and many cultures had women in the military as a matter of course, just not in as high numbers as men).
Batman: Arkham Asylum only has Harley Quinn, Poison Ivy, and Dr. Young, along with some very briefly seen doctors. Batman: Arkham City manages to be worse overall: despite the massive number of new characters added the only new female characters are Catwoman and Talia al Ghul, and while the former is playable the latter falls victim to Stuffed into the Fridge, Harley does nothing of importance, and Ivy is little more than a cameo.
Of the gang of playable characters in Borderlands, three are male, with a fourth man driving the truck, and one is female - introduced as "The Siren," which is barely a gnat's whisker away from simply calling her "the token girl." The vast majority of enemies are male, too. Or arguably, in the case of the skags, not sexually dimorphic.
Borderlands 2 continues the trend, three male characters and 'the siren'. Both games include a Voice with an Internet Connection named Angel who guides you through the game, as well as Mad Moxxi. The second includes Ellie, a mission-giver, and has all four of the original characters, and another female character class available as a preorder bonus or DLC, the Mechromancer.
Borderlands: The Pre-Sequel! averts it; two of the playable characters are male (okay, one's a robot, but everyone including himself refers to him as male) and two are female. The balance is kept with DLC characters "Jack" and Aurelia.
In Bully, each social clique has only a single female member versus about half a dozen male members.
In City of Heroes the main cast of NPC heroes, the Freedom Phalanx, has only two women, Numina and Sister Psyche, who ended up marrying one of the others, Manticore. The villain groups in Paragon City are almost all male, with two exceptions (there seems to be a pattern here...), the Carnival of Shadows and the Knives of Artemis.
Command & Conquer: Red Alert has two female characters — but since they are split by side, one of them isn't really part of the ensemble for the other side's campaign (especially on the Allied side — Tanya does make a few appearances in the Soviet campaign).
One of the 4 Horsemen in the Darksiders series named Fury is the only female horsemen and she has yet to make her debut in the game, only in the comics. Uriel and Lilith are also the only known female characters on the heaven and hell side respectively.
The campaigns for the first game and it's expansions only have one female character each, who is always an Eldar Farseer. Initially the only female unit is the Howling Banshees, but Dark Crusade adds the Harlequin and Soulstorm adds the Wyches. Soulstorm also tips the balance slightly by introducing the Sisters of Battle, who only have two male units, but they're still vastly outnumbered.
The second game has Idranel on the side of the antagonists (killed off in the first campaign) and Derosa on the side of the protagonists (one of the Mission Control members, who is nowhere to be found in Retribution). The Eldar campaign in Retribution has effectively one female character out of three (there's technically a second female character, but she has no lines), and the Imperial Guard campaign has Adrastia.
In Diablo I, only one of the three (the Rogue) classes was female. The Hellfire expansion added the male monk class by default, plus mildly altered remakes of the Warrior and Rogue that could only be unlocked by futzing with a system file. Diablo II evened the gender balance a bit with three female classes and four male ones. Diablo III removes the problem entirely by allowing the player to be either gender for all classes.
The series has only a few female Kongs: Candy Kong was the first, a vaguely fanservicey monkey who helps the player. Dixie Kong was introduced as Diddy's girlfriend, simultaneously with the grandmotherly Wrinkly Kong, and Tiny Kong was the only female member of Donkey Kong 64's Five-Man Band. Similarly, the Kremlings were always male in the games, and it wasn't until Barrel Blast that females were finally featured (specifically, Kass and Kalypso).
Dragon Quest VIII has Jessica, the only female playable character in a group of 4. She may be the Squishy Wizard but she has some of the more powerful weapon attacks. Though she does have some interesting costume changes. She's also the third character you get and the only one who can throw the big blaster spells. And there's also Princess Medea, but...
Drakengard: Aside from professionally Damsel in Distress Furiae, the only female character of note is Arioch. Who is a deranged, barren elf who eats children. She isn't even the worst person in the party, which includes a sociopathic mass murderer who routinely kicks his own allies in the head, a senile, racist old man, a pedophile, and a six-year-old boy who dooms the world out of petty spite.
All three entries of the Mother series has had three guys and one girl in the main party (or in Mother 3's case, two guys, a girl and a dog), the girl being the psychic powerhouse.
Contrast EverQuest, where female characters seem to outnumber male ones. Both Everquest and Everquest 2's main characters, Firiona Vie and Antonia Bayle respectively, were female. Firiona's nemesis, Lanys Ty'Val, was female as well.
Everybody Edits has the "Female Smiley" out of all of them, though the Summer Girl and Helen of Sparta were introduced later.
Fallout allowed you to choose your character's gender, but of the four recruitable NPCs only one was female. In Fallout 2 it got worse, with eight recruitable males, four dogs, a robot...and one female human, who was literally worse than useless (useless in a fight, can't gain levels, takes up a party slot and won't leave unless you kill her or sell her to slavers. The being said, some quests in the game were more easily completed if you were a woman. It is debatable whether this helps, but it certainly won't pass The Bechdel Test.
Fallout 3 is somewhat better in this regard, having two female recruitable NPCs who are relatively useful. However, they are still in the minority (there are three male companions, as well as a genderless (formerly male) super mutant, a male dog and a robot with a male voice).
Fallout: New Vegas has two recruitable female characters of comparable use with a formerly female nightkin supermutant (which used to be a sweet old granny.) Four of the remaining five are males, among them a ghoul and a cybernetic mutt.
The Fallout Bible mentions Vault 68, populated with 999 men and only one woman, and Vault 69, with 999 women and only one man. It is never mentioned what happened in these vaults, but considering the tone of the games and the other vaults, they probably didn't end well.
The Fatal Fury series introduced its first female fighter with the ninja girl Mai Shiranui in Fatal Fury 2. Blue Mary was introduced in Fatal Fury 3 to balance things out, followed by Li Xiangfei in Real Bout 2 and Tsugumi Sendo in Wild Ambition. Mark of the Wolves only had two female fighters (B. Jenet and Hotaru) out of a roster of 14 characters.
The Final Fantasy series has played with this trope throughout its entries:
Of the six character classes in Final Fantasy I, only the White Mage looks female (and the original White Wizard graphic◊ confirms White mage as a male Bishōnen). It's possible to see all of the characters as androgynous to be female and the remakes give most classes both male and female names.
The original version of Final Fantasy III stars the all-male Onion Knights; the remake for the DS makes one of them a girl.
Notably, every game since Final Fantasy IV has had exactly three female characters in the playable cast, regardless of the total cast size. This is explicitly referred to as the Three Females Rule in Squaresoft fan circles. This even extends to entries that don't follow The Smurfette Principle, like Final Fantasy V (three women, two men) and Final Fantasy X-2 (an all-female party of three). Note that later games have gravitated toward a total playable cast size of 6, thus equalizing the gender balance while still following the rule.
This is obvious in the crossover Dissidia. Terra is the only female on the protagonist side in the main storyline, besides the goddess Cosmos herself, entirely because the roster is composed of only the main characters of each game, and Final Fantasy VI is the only one to have a female lead. Secret fighter Shantotto does get a storyline all to herself. The side of evil is slightly fairer with Ultimecia and The Cloud of Darkness in their ranks, but the latter is questionable since "she" is technically female in physical form only and tends to talk like an old man. It has the same problem that most of the main villains in the series are male. The Dissidia Duodecim additions of Tifa Lockhart, Yuna (who was the original pick to represent her game before settling on Tidus), Prishe and Lightning alleviate this somewhat on the heroes' side, but the cast is still overwhelmingly male.
While Fire Emblem has a diverse cast of genders in most games, some of them have this problem with the villains. General Petrine of Daien is the only woman among the Four Riders, and the only other female villain in the game is Ena, who pulls a Heel-Face Turn after the heroes defeat her at the capital. Fire Emblem: The Sacred Stones had only Selena on the villains roster and even then Selena remains loyal to her homeland, not being one of the 3 truly evil generals. Fire Emblem (aka Rekka no Ken) was a little more balanced, though it still had more male villains than females and two of the "females" (along with one of the "males") are explicitly genderless.
Anya Stroud is the only female who fought alongside Marcus in Delta Squad in Gears of War 3.
The only women in the entirety of Half-Life are the black-clad assassins who never speak and only appear in two areas. The Fan RemakeBlack Mesa very deliberately added a lot of female scientists to address this imbalance.
In Halo: Combat Evolved Cortana is the only female in the entire game other than the pilot, Foehammer, and some other generic unnamed pilot. Noble Team in Halo: Reach has only one female Spartan, unless you make Noble Six female.
Heavy Rain: Four playable characters, one female—complete with relationship conflicts with another main and sexualized role (which you can undermine later, but still).
Played straight at first in Killer Instinct then interestingly averted later by Word of God: initially Black Orchid was the only female on the original cast of KI but when development started on season 2 of the 2013 game, it was revealed Riptor is and always was a female, meaning the original KI actually had two female fighters.note Of course Riptor being a human-raptor hybrid meant her gender was never really relevant in the first place anyway.
In the Kingdom Hearts games, while there are a small handful of important female NPCs, when it comes to the playable characters, the three main characters are all male, and there's only one female Guest Star Party Member in each game; Ariel of The Little Mermaid in the first one, and Mulan in the sequel. There's also Organization XIII. Out of thirteen members, there is only one female. Another female, Xion, seems to be added in 358/2 Days, but her status ends up rejected in more than one way.
The Two Guys and a Girl pattern ensures alot of this, with Kairi, Xion, and Aqua each being the only girl in a friendship circle.
Worse still, those five girls end up having little role in the plot. Finding Kairi is Sora's main character motivation, but character-wise she gets sidelined a lot. Namine has that problem as well, though she at least takes a supporting role in helping Sora recover from the events of Chain of Memories, though that gets overshadowed by DiZ and Riku in most occasions. Larxene exists merely as a satellite to Marluxia, who managed to be little more than a Filler Villain for Chain[[note: Fittingly, he was meant to be a woman as well, before the developers realized that would be sexist]]. Xion and Aqua are the two characters that break out of this role the most, with the former being both a legitimate character motivation and love interest, and serving the role of Final Boss for the game she appears in, though she's not fully female, while the latter is actually a playable protagonist in her game.
Chizuru, Shermie, and Shion are the only female boss characters you will face in The King of Fighters series, in 96/2003, 97, and Xi respectively.
The playable characters in both Left 4 Dead and its sequel consist of three men and one woman - neither is The Chick, however, and they are both distinctly different from each other. This is explained as the gene to be resistant to The Virus is recessive and carried on the x-chromosome. Women need two copies of the gene, while men only need one, explaining the genetically sound 3:1 ratio.
Depending on the game, Zelda may be the only important female character in the series. Other games invert the trope, such as Ocarina of Time, Twilight Princess and Skyward Sword. The former two have 3 main protagonists (Link, Zelda and Navi/Midna) while the later has 5 (Link, Zelda, Fi, Impa and Hylia) and Link is the only male of all three groups.
The entire Zora race suffers from this. Most of the notable Zora characters as well as the unnamed NPC's there is usually only one female among a sea of muscular-bodied males.
In Live A Live, most of the characters you control are male, except two: Prehistoric Chapter's Bel, who won't be coming for the Final Chapter, or Kung-Fu Chapter's Li Kuugo, who'll only appear in the Final Chapter if picked as the star pupil (otherwise she got Killed Off for Real).
Mass Effect applies the trope to species, not individuals (on that regard it is largely gender balanced). You never see a female turian or batarian, although female turians are shown in the Mass Effect: Evolution comic. It's difficult to determine the gender of volus and hanar, but all the ones we've met have masculine voices and none have been suggested to be female. One female elcor can be heard, but not seen, in the Blasto 6 commercial. The asari are a mono-gendered species, but they all look and sound very much like human women. BioWare has said this was so they wouldn't have to design separate character models for each race. The lack of Female Turians is finally averted in the Omega DLC for the third game, featuring a female Turian biotic named Nyreen, and later the multiplayer mode added female turians as well.
The Mega Man series, as a whole, does this constantly. There is a grand total of two female characters in the entire original series - Roll, who took until 10 to get a single plot-significant action to her name (and is never playable except as a joke — she's a housekeeping robot), and Mega Man 4's Kalinka, who exists entirely to be kidnapped. As for the villains, they had to be male because of the naming scheme — every Robot Master is called <word> Man. This has changed with the introduction of Splash Woman in 9...then 10 went back to the status quo.
The X series has only a couple, mostly in noncombat roles as well — Iris was Zero's love interest and apparently not a combatant (though she did fight at the end — against him, and she dies by his sword), Alia plays mission control in later games, and a few of the bosses are feminine. X8 changes this slightly, as the three female operators are unlockable as bonus characters, each one emulating one of the main (male) characters to varying degrees of success. Alia isn't all that useful as she lacks X's ability to use different armor parts, but Layer is every bit as powerful (and badass) as Zero, and Palette lacks only Axl's ability to copy enemies (which is mostly used for the purpose of finding items rather than combat).
The Zero series began to turn the tables. The series had Ciel (the most important non-player character), Leviathan (one of the four Guardians, a Quirky Miniboss Squad that evolved), Neige, and many of the bosses and Resistance NPCs are female.
The Battle Network series inherited the same problem as the original, since most of the Navis are based on original series Robot Masters. However, there are lots of female human characters to make up for it.
Rockman Online has four announced characters: X, Zero, Duo, and Cinnamon. Guess which one's the token chick.
Metal Gear follows this trope almost religiously. In the first Solid game Sniper Wolf is the only female FOXHOUND member. In Sons of Liberty Fortune is the only female Dead Cell member. In Snake Eater The Boss is the only female Cobra unit. In Guns of the Patriots Meryl is the only female member in Rat Patrol 01. In Peace Walker, Paz, Amanda and doctor Strangelove are the only female members in the MSF in terms of storyline, although you can recruit more female soldiers into your unit to even the balance. In Rising Mistral is the only female member of the Winds of Destruction.
Despite being the flagship Action Girl of the video game world, Samus Aran of Metroid fame managed to become the Smurfette in her own series in Metroid Prime: Hunters. Six new bounty hunters were introduced, all of them male or ambiguously so. She's also the only Hunter without a unique weapon, unless you count the fact that her missiles home—but this may be due to the tendency of game heroes not to specialize than any smurfiness. Metroid Prime 3: Corruption is more fair, as one of the three new hunters is another female.
The only female character in Modern Warfare is your fellow Cobra pilot "Deadly" in the first game. Mostly justified by being a military game; while women are no longer barred from joining in a lot of places, real life militaries are still heavily male dominated.
Let's see, Mortal Kombat... For the first game, the creators realized they didn't have any female fighters in their roster, so they changed the character of male Kurtis Stryker into female Sonya Blade (Stryker would become a fighter after all in the third game). This made her the only female out of 7 playable characters and 10 fighters overall. Later games have made sure to include female playable characters from the start, with the ratio male:female about 5:1. As for the various factions and species, most of the time there are more (known) male characters than females, the exceptions being the saurians (1:1 or 1:2), the demons (2:5), and the vampires (0:1 or 1:1). Interestingly in case of the vampires, initially there were supposed to be a female and male vampire introduced in Deadly Alliance, but the male was dropped because of time constraints.
Nezumi Man has Wave Nezumi, the only female boss of the eight. Kind of a coincidence then that her powers are the same element as Splash Woman's.
In One Piece Mansion, Raspberry is described as being the only female in Syndicate 5.
Overall, the major Pokémon characters tend to lean in favor of males; only in Diamond and Pearl was a female Champion introduced, and it took until Black and White to introduce a female Pokémon Professor, and even then she got majorly sidetracked by a male professor as her father. In spite of this, the Gym Leaders and the Elite Four are normally reasonably balanced and the player has been able to play as a boy or a girl since Crystal, with the developers having planned to implement female player characters since the beginning. Ruby/Sapphire and Black/White also have female rivals. The followinggames have both included female Champions, though, as well as at least 2 female supporting NPCs.
In Rage, Elizabeth is the only known female Resistance member.
Most Resident Evil games avert this, but while Resident Evil has two major female characters, they are the sole female members of their respective STARS teams (Jill for Alpha team, Rebecca for Bravo team). Weirdly, in early games, there are almost never any female zombies (the first game only had male zombies, while the second and third games had only one female zombie model among a slew of male models); this is averted by the time Resident Evil 0 rolls around, and the Gamecube/Wii remake of RE1 added Lisa Trevor.
Rachel Parker in the Resistance series is the only female recurring survivor.
In Robopon, in the first game, Miss Amron is the only female Legend out of seven. (Kamat may or may not be a girl). This is averted with the Elite 8: All of its members are girls.
In Scribblenauts Unlimited, Maxwell has many, many siblings you can unlock and play as. All but one of them are brothers, and the one sister is the Damsel in Distress.
Sengoku Basara spinoff fighting only had Oichi as the only "true" playable female character of the sausage fighting fest. The rest of the girls are delegated to backup.
In the first Shin Megami Tensei, all of the Seraphim (Michael, Uriel, Raphael, and Gabriel) were presumably male, but the second game reveals Gabriel is a girl, and all subsequent SMT and Persona games featuring Gabriel retain this.
Sonic the Hedgehog was never character-heavy in its early games, but no female character was even seen until Amy Rose, who looked like a little pink Sonic in a dress. More characters have been introduced as the cast has expanded, but the majority have been male. Of the Deadly Six in Sonic Lost World, only one (Zeena, the green one) is female.
Spyro the Dragon had no important female characters at first. Then along came Bianca and Elora, with the first being a sort of villain and the other just a love interest, then Sheila, a female kangaroo. Even in the Legend of Spyro series, Cynder is the only important female character, with no others present. Largely continues into Skylanders; out of 80 total Skylanders through 3 games, there are only 14 female characters. Only one of the 8 Giant Skylanders is female, none of the Swap Force Skylanders is female, and it wasn't until the third game that a female Fire Skylander was added. At least the Swap Force case has a reason due to the Lego Body Parts mechanic; mixing males and females would be... awkward.
Starcraft had exactly one named female character: Sarah Kerrigan, who is betrayed but rapidly becomes the queen bitch of the universe as the Queen of the Zerg. The expansion set added the Protoss matriarch Raszagal (the only female Protoss for the next ten years). Starcraft II expands the universe a bit, including adding supporting female human characters, but with Raszagal dead, the role of "only female Protoss" is inherited by Executor Selendis, who will is the protagonist of the second expansion set. Starcraft: Ghost's main character was to be a female Ghost, not unlike Kerrigan.
The Star Fox games follow the principle. The original game, and its remake, Star Fox 64, featured an all male membership in the title team (bad jokes about Slippy's Ambiguous Gender notwithstanding) and only one female character period—sometime ally Katt, who assisted you in Zoness and Sector Z. It wasn't until Star Fox Assault that the team gained a permanent female member: Krystal from Star Fox Adventures. The unreleasedStar Fox 2, however, would have added two female characters to the roster - Genki Girl Fay and Action Girl Miyu. And in Command, there are a solid 4 females: Krystal, Kat, and newcomers Lucy (Peppy's daughter) and Amanda, Slippy's female love interest. There is even an all-girl mission.
Both Star Wars Battlefront I and II feature at least four factions and have as much as three female characters, the generic Rebel Sniper class (which is excluded in a few maps), Princess Leia, and Aayla Secura, the latter two both hero class characters limited to appear in as much as four maps (if you count Hero Assault). If you own the Xbox version there is Asajj Ventress hero character from the DLC.
The first iteration of Street Fighter II had only one female warrior out of twelve fighters, Chun-Li. (She is often called the First Lady of Fighting Games by fans, as she was the first female of the genre, period. One of Chun-Li's win quotes in Tatsunoko vs. Capcom, which has a roughly even male/female mix, makes fun of this: "I remember when I was the only girl on the roster.") This gradually changed through the course of the series with the introduction of Cammy in Super Street Fighter II; Rose, Sakura, R. Mika, Karin, Juni and Juli in the Street Fighter Alpha series; Ibuki, Elena, and Makoto in the Street Fighter III series; and Crimson Viper and Juri in the Street Fighter IV series.
The cast of crossover characters from Final Fight initially featured four characters, all male, but this changed with the addition of Maki (from Final Fight 2) in the portable versions of Alpha 3.
The Super Mario Bros. games' only recurring female character was Princess Peach, who was usually a Damsel in Distress. This changed as Princess Daisy and Birdo became full-fledged main characters and with the introductions of Toadette, a feminized Toad, and Rosalina, both of which were somewhat less stereotypical than Peach. The ratio still heavily favors males.
The first two Mario Party games had Peach as the sole playable female character. This was changed in Mario Party 3 when Daisy was added to the cast.
On the villain side, the first evil female was the single girl of the Koopalings, Wendy O. Koopa. Captain Syrup showed up later as Wario's nemesis, and some stage bosses were female (Naval Piranha). Lately the villainous ladies have become more numerous with Cackletta, the Shadow Queen, Princess Shroob and Elder Princess Shroob, Mimi, the Shadow Sirens, and Robirdo.
In the next, out of 13 new characters, Super Smash Bros. Melee introduced three new females, one of whom teamed with a male character as the Ice Climbers. Super Smash Bros. Brawl didn't add any females to the cast, though it did make the gender of Samus and Sheik more visible.
The Wii U and 3DS iteration manages to avert this trope: While Nana was removed, Sheik and Zero Suit Samus were made separate characters, the Wii Fit Trainer is female by default, there's the option to play as female Villagers, female Robin or Wendy, Miis can also be female and finally, Rosalina, Palutena and Lucina were added. That makes it roughly 12 female characters in all.
Three crossovers which come to mind that have larger amounts of females than others are Super Puzzle Fighter II Turbo, Pocket Fighter/Super Gem Fighter Mini Mix, and Cross Edge.
Most Super Robot Wars games allow the player to choose between an equal number of male or female original characters. While this doesn't quite help the ratio among the licensed games, it makes for a more or less even mix among characters in the Original Generation series.
Team Fortress 2: The only obvious woman in the game is "The Administrator", aka the angry voice that screams at you during rounds. Admittedly, the Pyro may be female (or genderless, for all we know), and the comics also have the character Ms. Pauling, but if you look just at the game, it follows this trope.
Torchlight has the same gender ratio as Diablo I (not surprising, considering the similarity between the two games and many of the same developers). Also like Diablo, the lone female happens to be the physical ranged damage dealer.
Several of the Ultima games have a less-than-favorable ratio. While the eight "Companions of the Avatar" had a 4:4 ratio, the females generally had worse stats. (By design in Katrina's case, as Shepherds by design aren't supposed to excel.) The trio of Iolo, Dupre and Shamino (all male) also kept gaining prominence over other characters as the game went on. The eighth and ninth games even disallowed playing as a female main character!
Rather smurfy is the Warcraft series, especially Warcraft III: Out of twelve heroes, only one, the Priestess of the Moon, is female, and the consensus is that she is the worst of them all. You mean they couldn't at least squeeze a Jaina Proudmoore lookalike in there, given that she's already a custom model representing the hero type? At least there are actually female units, and the expansion The Frozen Throne added three female heroes — the Warden, the Dark Ranger, and the Naga Sorceress — who were at least decent.
Looking at the races themselves, only the Night Elves have a significant amount of female units. The humans have the sorceress, orcs have nothing at all and the undeads have the banshees. And there are no female neutrals either, unless you count the High Elven archers.
The earlier games in the series had no female characters until Warcraft II: Beyond The Dark Portal, and then you got only one: Alleria Windrunner, a unique unit and Sylvanas's elder sister. Warcraft: Orcs and Humans had a half-orc, half-human (who was later retconned into half-Dranei) girl, Garona Halforcen, present in one mission.
The Orc gender balance was also acknowledged in World of Warcraft in that the orcs actually were sexist. Despite being every bit as aggressive and strong as the men, women were denied combat roles. Thrall changed that between WC3 and WoW.
Wild ARMs 1 and 3 both follow this trope. Each of the two games has one playable female character (teamed up with two or three males), though Cecilia and Virginia are each portrayed as the one calling the shots. Wild ARMs: Alter Code F, a remake of the first game, alleviated the gender issue by adding Calamity Jane and Ema to balance the cast (Zet, a guy, is also recruitable).
Wolfenstein 3D has one single female in both series, who is a boss that looks almost exactly like her brother and has a low voice.
Four main playable characters in The World Ends with You, and you can count how many of them are female on the single hand of a blind butcher.
Citrine is the only female URTV shown in the XenoSaga trilogy, even though she stated there are 8 others like her.
Many early computer games would let the players choose their gender (as well as, often, other attributes like name, race and age) at the start of the game (unless you were a Featureless Protagonist, of course). As the amount of assets (graphics, voice acting, and sometimes even onscreen actors) needed to portray player characters increased, many studios discreetly dumped this feature. Modern games that let you choose a gender offer varying amounts of plot and gameplay branching as a result of the choice.
Final Fight 2 and 3 has Maki and Lucia respectively. Both are Fragile Speedsters naturally, but Lucia is actually a bit stronger than Guy (the token speedster in that game).
Gauntlet has three male (Warrior, Wizard, Elf), one female (Valkyrie). Sequel Gauntlet Legends averts this by changing the androgynous-looking elf to a female elven Archer. Dark Legacy falls back in when adding four more characters to the existing four: three male (Dwarf, Knight, Jester) and one female (Sorceress). As well, the breasts on all the women became about twice the size of their heads. Seven Sorrows then goes back to the original four characters. Get Medieval, a Spiritual Successor by Monolith Productions, kept a 2:2 ration by turning the Wizard into a naughty sorceress whose every line was a Double Entendre. (Okay, some were even single ones...)
Both Left 4 Dead games have one female in a group of three males. In the sequel, the two groups meet so it's two girls with six guys. Most of the NPCs in the games are male, including the special infected until the Spitter and the female version of the Boomer were introduced in the sequel. The common infected, however, are both male and female.
On a related note, many other fighting games fall victim to the same problem, but not because they're drawing from other canons. It is rare to find more than a few female characters available to play out of an otherwise large collection. Generally, the female characters are also notably weaker than the male characters. This is parodied in VG Cats — here.