The main antagonist could be a powerful figure who has a vendetta against the Elric family. Now that Edward is a girl, they think it's the perfect time to strike. They might try to isolate Edward from his friends and allies, using the fact that his new form is causing some confusion and unease among those around him.
Perhaps a new alchemist who is jealous of Edward's skills, even in his new form. This antagonist might see Edward as a girl as an easy target to discredit. They could spread rumors about how Edward's transformation has made him less capable in alchemy, when in fact it's just their way of trying to undermine him.
One possible plot could be that Edward, now as a girl, has to deal with the different reactions of his friends. For example, Alphonse might be a bit confused at first but quickly adapts and becomes very protective. Edward could also face new challenges in his alchemical studies as some traditional alchemy is male - dominated. And he might have to struggle with his own self - identity, trying to figure out if he still has the same goals and values as before the transformation.
It could be an evil wizard who was the one who actually caused Gumball to turn into a girl in the first place. The wizard has some ulterior motives, like using Gumball's new form to gain power or to cause chaos in the town. He tries to prevent Gumball from finding a way to turn back and keeps creating obstacles for Gumball and her friends.
It could be a villain who is obsessed with creating chaos through strange transformations. This villain might have targeted Deku specifically because of his status as a rising hero. They want to see how Deku will cope with being turned into a girl and use it to undermine his confidence and hero image.
Ganon could still be the main antagonist. Even though Link has turned into a girl, Ganon's goal of taking over Hyrule remains the same. He might underestimate Link in her new form, which could give Link an advantage. For example, Ganon might not expect the girl - Link to be as strong or resourceful as the male Link, but she proves him wrong.
Perhaps a jealous classmate who has always been in Izuku's shadow. Now that Izuku is a girl, this classmate sees an opportunity to undermine her. They spread rumors about how Izuku's transformation is some sort of cheat or that she's not the same reliable person she was as a boy. This classmate's actions and attempts to sabotage Izuku would make them the main antagonist.
It could be a jealous trainer who doesn't like the attention that girl - Ash is getting. This trainer might try to undermine her at every turn during Pokemon battles.
There could be an ancient evil spirit that was released when Aang turned into a girl. This spirit feeds on chaos and the disruption of natural order. It sees Aang's transformation as a sign of the world being out of balance and tries to make it even worse. It might target Aang specifically because he is the Avatar and his new form gives it an opportunity to create more disorder.
Maybe a new character could be the main antagonist. This character could be jealous of Sonic's speed and popularity. So, when Sonic turns into a girl, this antagonist sees it as a chance to frame Sonic for various crimes in this new form. This would make Sonic's friends doubt him and isolate him, all part of the antagonist's plan to take Sonic's place as the hero of their world.
There could be an organization that wants to keep Ki a secret from the world of alchemy. They see Edward's attempts to learn Ki and potentially bridge the gap between the two as a danger. So, the leaders of this organization send their agents to stop Edward, and the most powerful of these agents could be the main antagonist in the fanfiction.
It could be another alchemist who wants to use this new energy for evil purposes. This alchemist might see Edward as a threat to his plans and constantly try to stop him from learning more about the energy.