Perhaps an old acquaintance of Ryuuji's who has some unresolved issues with him. When Ryuuji turns into a girl, this person sees it as an opportunity to get revenge in a more devious way. They might try to manipulate the situation and the people around Ryuuji to make her life miserable, all while hiding their true motives from others.
In some cases, it might not be an individual but a group. For example, a clique of girls who have very strict ideas about what it means to be a girl. They don't accept Ryuuji as one of them because she was originally a boy. They constantly exclude her from their activities and try to make her feel like an outsider, which creates a lot of conflict and drama in the fanfic.
One possible plot could be that Ryuuji wakes up one day as a girl. He, now she, has to deal with the reactions of her friends like Taiga. Taiga might initially be shocked but then grow more protective. Ryuuji would also have to adjust to new social dynamics at school, like how the boys interact with her now and how she fits in with the girls. She might struggle with wearing different clothes and having different expectations placed on her.
It could also be a new villain that is specifically interested in Sonic because she is now a girl. Maybe a villain who has some sort of vendetta against female heroes or wants to use Sonic's new form for some evil experiment. However, Dr. Eggman is so iconic in the Sonic series that he would be a strong contender for the main antagonist role even in this fanfic scenario.
Another possibility is that an alien race that Ben has previously encountered and thought was friendly, now turns against him/her because of the change in gender. They might have some strange beliefs or customs that make them view Ben's new form as a threat or an abomination, and thus they become the main antagonists in the fanfic.
There could also be new antagonists. For example, some of the more traditional wizarding families who are against the idea of a female Harry. They might see her as a threat to the old - fashioned ways of the wizarding world and try to undermine her.
It could be Vilgax. He might see Ben 10's new form as a weakness and try to take advantage of it.
It could be a character who is against the idea of Percy being a girl. Maybe someone who believes in strict gender roles in their world and sees Percy's transformation as an abomination. For example, an old - fashioned wizard or a powerful deity.
It could be Morgana. She might see Merlin's transformation into a dragon as a threat to her own power and plans. So, she tries to stop him from fully becoming a dragon or tries to use his new form for her own evil purposes.
It could be a rogue AI that wants to use Chell for its own malicious purposes. Maybe it sees Chell as a key to accessing some powerful technology or information.
It could be an ancient and powerful god who has long been plotting against Percy. This god might be jealous of Percy's power and popularity, so he devises a plan to turn Percy into a killer, knowing that it will lead to Percy's downfall and his own rise in power.
Maybe the main antagonist is a group of demon hunters. They sense Ciel's transformation into a demon and see it as their duty to eliminate him before he becomes too powerful. They hunt him down relentlessly, making Ciel's life as a new demon very difficult.