Another possible main antagonist could be an envious noble from the court. In the fanfiction, this noble could discover a way to manipulate time and create situations where Cinderella looks bad in front of the prince. They might try to insert themselves into the story and take Cinderella's place. For example, they could make it seem like Cinderella was rude to the prince in a previous encounter by altering the time - line slightly. This would cause all sorts of problems for Cinderella as she tries to set things right and keep her relationship with the prince intact.
The stepmother is an obvious choice. In a time - twist scenario, she could use her knowledge of the past to try and prevent Cinderella from ever going to the ball in the first place. Maybe she finds a way to change the events that led to the fairy godmother helping Cinderella.
The stepmother could still be the main antagonist. But instead of just being mean in a traditional way, she might be a powerful witch who is trying to steal Cinderella's natural magic for herself. So she keeps Cinderella down to weaken her magic.
The main antagonist might be a minor god who has a grudge against Cinderella's unknown demigod parent. This god uses Cinderella's stepmother as a puppet to keep Cinderella from fulfilling a prophecy that would lead to the god's downfall. He or she would do everything in their power to stop Percy Jackson from helping Cinderella discover her true self.
Cinderella's fairy godmother could also turn out to be the antagonist. She might have given Cinderella false hopes and used her to fulfill some self - serving prophecy. Maybe she has her own dark secrets and is manipulating Cinderella all along.
Another option could be an evil wizard in the Cinderella world who sees Naruto as a threat to his control. He might try to keep Cinderella in her oppressed state to prevent her from getting closer to Naruto, who has the potential to bring new ideas and power that could undermine the wizard's authority.
Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
It could be an ancient evil ninja who was sealed away long ago and somehow gets released in the time chamber. Naruto has to face this powerful foe while also dealing with the time - warped environment of the chamber.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
Cell could be a great antagonist. Even if Gohan goes back in time, Cell might still find a way to exist. Maybe he adapts his plan to absorb the Androids earlier in time. Gohan would then have to face a more powerful and unpredictable Cell, who could potentially change the timeline to his own advantage.
Frieza would be a great antagonist. If Goku goes back in time to a point before Frieza was defeated, Frieza could be an even more menacing force as Goku might not have all the power - ups he had in the original timeline. He'd have to rely on his wits and basic training more.
It could be another character who also has some time - related powers but uses them for evil. This character might try to steal Percy's time - controlling ability or use their own powers to disrupt the timeline for their own gain.