I just covered male characters in girl franchises, they got sold less jut like girl characters in boy franchises, hence little toys made of them or just one girl per franchise.
April O'Neil (Ninja Turtles)
April was in the original Mirage Comics and she has been in every incarnation of the Teenage Mutant Ninja Turtles (or Hero Turtles in the UK) except for Saban's Next Mutation. In the 80's-90's cartoon and first three movies, she was a news reporter. In the 2000's series and comic, she was assistant to Dr. Baxter. She has been heroic in most incarnations even though sometimes she needs help.
Venus DeMilo (Ninja Turtles)
She was the only female turtle and only appeared in one incarnation Saban's Ninja Turtles: Next Mutation. Her real name was Mei Pieh Chi and she was raised in the Chinatown district and wasn't the turtles' sister, in order to let open the potential of a love interest. Co-creator Peter Laird hated her and didn't like her because of the idea that the Ninja Turtles were the last ones of their kind and the idea of a female would give potential to survival of their species. Fox Kids, which aired Next Mutation, urged for her creation.
Arcee (Transformers)
Although a group of Female Autobots had already been featured in one episode of the original cartoon series, Arcee quickly became the most famous due to her position as a recurring cast member following her introduction in The Transformers: The Movie. The female Transformers did not appear in the American Marvel comic book series, where it was specifically stated that Transformers do not have genders. Arcee was initially set to be in the 2007 Transformers film, but due to negative fan reaction and to the fact that there was not enough time in the movie to explain the presence of a "female" in a robotic race, she was dropped from the script and replaced with Ironhide. She did appear in the Revenge of the Fallen. She mostly appears as Pink except in the current Transformers: Prime where she is blue.
Blackarachina (Transformers)
She first appears in the 1996 series Transformers: Beast Wars where she is part of the Predacons. Her toy was the first female Transformers toy to be produced. She later becomes a good guy and is one of the main characters in Beast Machines. In Transformers: Armada, she was an autobot known as Crystal Widow. In Transformers: Animated, she was initially Elita-1 (which was Optimus Prime's boyfriend in the first series) and wanted revenge on Optimus. In the current Transformers Prime, Airachnid is a homage to her.
Pink and Yellow Rangers and other assorted ones (Power Rangers)
As you may know, I am obsessed with the Power Rangers and I have my blog Henshin Grid. In the past 19 years, there has been various versions of Power Rangers. Most teams have a Pink and Yellow Ranger. In the original series Super Sentai, most Yellow Rangers have been male so that explains why some Yellow Rangers had no skirts. So far there has been 2 blue female rangers, 4 white, and 2 silver. Soon there will be a red female ranger in Power Rangers Super Samurai, making 2 female Red Rangers in the franchise. They make less female figures because of the belief that they sell less. It used to be that Pink Ranger got motorcycles and other accessories but now has been reduced to just one or two figures.
Teela (He-Man)
I mentioned Bow of She-Ra, Teela was He-Man's Gal Friday/Love Interest. She was a jerk to Adam and kind of liked He-Man. Another female in the series was her mother the Sorceress. In the 2002 reboot, Teela was the leader of the Masters of the Universe.
Gwen Tennyson (Ben 10)
She is depicted as snobbish and very mean due to her young girl attitude.She is Ben's cousin. When she is 15 in Alien Force, she's not nearly as fiery or short-tempered as before, Gwen is
still always looking out for her first cousin.
Amy Rose (Sonic)
Known earlier as Rosy the Rascal, she debuted in Sonic CD (1993) as the third recurring protagonist. Amy Rose is based on one of Kenji Terada's characters. She is a pink, female, anthropomorphic hedgehog who is obsessed with Sonic, even going so far as to declare herself his girlfriend. She has been trying to win his heart in everything from the series' games to animated TV shows and comics. 
Misty (Pokemon)
Misty started out as part of the original trio of Ash, Brock and herself. She specializes in water-type Pokemon. She had more focus in the Anime. The book The Japanification of Children's Popular Culture
described Misty's portrayal in the anime as a mother figure, calling her
a "nurturing component" for the original trio of herself, Ash and Brock.
Princess Toadstool/Peach
Mario's love interest and Damsel in Distress in the franchise. She is not a playable character in the main Super Mario games except for the American NES Super Mario Bros 2. However, she is the main protagonist in Super Princess Peach and is a playable player in most Mario spin-offs such as Mario Party and Mario Kart. In most games she is portrayed as selfless, perky and generous.
Typically, she does not show an aggressive nature even when she is
fighting or confronting her enemies. However, in Super Princess Peach, she shows wild mood swings from Joy,
Sadness, Happiness, and Anger each of which give her a special ability.There is plenty more like Batgirl of Batman, Black Cat of Spider-Man and Black Widow of the Avengers, which are from the comics so I rather not put them here because they had their own focus comics and other incarnations.
