Another possibility is that the main antagonist is an evil scientist who was responsible for Ash's transformation in the first place. This scientist could be trying to create some sort of chaos in the Pokémon world by turning a well - known trainer like Ash into a girl. And now, Ash as a girl has to stop this scientist from causing more harm to the Pokémon world.
Perhaps a powerful sorceress. She could be jealous of Robin's connection to Batman and the other heroes, so she uses her magic to turn Robin into a girl as a way to humiliate and weaken him. The sorceress could then try to use Robin's new form to her advantage, like trying to make Robin turn against the heroes or something.
It could be Team Rocket as always. Since Ash is now a Pikachu, they might see it as an easy target to capture. They could have new gadgets specifically designed to catch Pikachu - Ash, and constantly try to get their hands on him throughout the fanfiction.
It could also be a new villain. Maybe someone who has been waiting for Sonic to be in a vulnerable state. This new villain could have a special power or weapon that is more effective against Sonic as a kid. For example, a device that can slow down Sonic even more or nullify his powers temporarily. They might target Sonic not just because of his weakened state, but also because they know that his friends will be distracted trying to help him get back to normal.
It could be Voldemort. He might see Harry's new snake form as a way to either use him for his own evil purposes or as a threat to his power. Since snakes are often associated with Slytherin and dark magic, Voldemort might try to control Harry.
The main antagonist could actually be Anakin's own self - doubt. Since he's in a child's body but has an adult's memories, he might struggle with feelings of inadequacy. This internal struggle could act as an antagonist, preventing him from fully embracing his new situation and using his abilities to the fullest. It could be a psychological battle within himself that holds him back more than any external foe.
The main antagonist could be a jealous classmate. This classmate is envious of Ron's friendship with Harry and Hermione. So, they find a way to use dark magic to turn Ron into a fiend, hoping to drive a wedge between them. However, as the story progresses, they realize the consequences of their actions are far more serious than they thought.
It could be Voldemort. He might see turning Harry into an elf as a way to weaken him. Since elves are generally seen as lower in the wizarding hierarchy, Harry in this form would be less of a threat to Voldemort in the eyes of many wizards.
One possible plot could be that Ash wakes up one day as a girl and has to deal with all the changes in his daily Pokémon adventures. For example, he might have to adapt to new clothing styles and different social interactions. His Pokémon might also react in various ways to his new form.
It could be a trainer who has a starter that has a type advantage over Ash's new starter. For example, if Ash has a Squirtle and the antagonist has an electric - type starter like Pikachu, they would constantly be in conflict. The antagonist might be jealous of Ash's skills or the potential of his Squirtle and try to undermine him at every turn.
Team Rocket is an obvious choice. They could use some new, devious hypnosis device to control Ash for their own gain, like trying to steal all his Pokémon.