Peter Parker from Spider - Man could be an interesting choice. Imagine if Peter was turned into a girl. He would still have his spider - powers, but would have to deal with the added complications of being a female superhero in a male - dominated world.
Frodo Baggins from The Lord of the Rings. If Frodo were to turn into a girl, it would add a whole new layer to his journey to destroy the One Ring. He would face different challenges and perhaps be treated differently by the other characters in Middle - earth.
Hermione Granger from the Harry Potter series could be an interesting character. Imagine if she was hypnotized to forget all her magical knowledge. Another could be Katniss Everdeen from The Hunger Games. Hypnotizing her to not be able to use her archery skills would create a whole new set of challenges for her.
Izuku herself is obviously a very popular character in this type of fanfiction. Since the whole story revolves around her transformation into a girl. Her friends like Ochaco Uraraka also tend to be popular as they often play important roles in Izuku's new life as a girl. Their relationship might change and develop in interesting ways.
Harry Potter and Luna Lovegood from the 'Harry Potter' series could be great for this. Harry is always in the thick of the action, focused on fighting Voldemort, while Luna has her own unique and dreamy way of seeing the world. An 'unexpected love' story could be that Harry, who has always seen Luna as a bit of an oddball friend, suddenly realizes he has deeper feelings for her during a particularly difficult time at Hogwarts, like when they are all in hiding and she brings a sense of calm and new perspective to him.
Darth Vader from the Star Wars Galactic Empire could be a great character in an empire crossover. His dark and powerful presence would add a lot of drama. Also, Emperor Palpatine. In a crossover with another empire, they could be the antagonists trying to take over the new empire. Another character could be Captain America from the Marvel universe. If you consider the United States in the Marvel world as an 'empire' of sorts in terms of power and influence, his sense of justice and leadership could be interesting when put against the values of another empire.
The moral might be about acceptance. In the story where the boy is turned into a girl, it shows that no matter what form a person is in, they are still a person. If the characters in the story learn to accept the transformed boy - now - girl, it teaches the readers to be more accepting of differences in general, whether they are caused by magic or just natural differences among people.
It could be a shy boy named Tim. Tim is often bullied at school for being different. One day, a magic spell turns him into a girl. At first, he is horrified, but as he starts to adapt, he realizes that he can be strong in this new form. He stands up to his bullies and in the process, becomes more confident whether he's a boy or a girl.
Some popular characters in boy girl battle series fanfiction are the boy who is a natural leader. He has charisma and is able to inspire others to fight alongside him. And then there's the girl who is an outcast in her own society but discovers she has amazing fighting potential. Her journey from being an underdog to a powerful fighter makes her a beloved character. Also, characters with unique weapons or fighting techniques, whether they are boys or girls, are always popular as they bring something new and exciting to the battles.
In some fanfictions based on 'Riverdale', Jughead could be seen as the bad boy and Betty as the good girl, and there are many stories exploring their relationship in that light.
Well, it could be about a scientific experiment gone wrong. A boy volunteers for an experiment that is supposed to enhance human abilities. But instead, there is a malfunction in the machinery or chemicals used. This causes his genetic makeup to change, and he turns into a girl. He then has to deal with his new identity, his family's reaction, and his own feelings about this sudden transformation.
Captain America could be a great character to use. He was a WW2 soldier himself, so it would be easy to create a crossover where he meets other soldiers from different parts of the war or different universes. Another one could be Indiana Jones. His adventurous spirit combined with the skills of a WW2 soldier could make for an exciting crossover. Also, Sherlock Holmes could be used. The WW2 soldier's practical knowledge and Holmes' deductive reasoning could lead to some interesting storylines.