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 a character who wants to use Percy - turned - Aku for their own evil purposes. Maybe a dark wizard who thinks that Aku - Percy can be the ultimate weapon to take over the world. This wizard would try to manipulate Percy's new form and powers to do his bidding.
It could be a fallen angel who is jealous of Percy's new - found angelic status and wants to bring him down.
It could be a powerful leader from another race who sees Percy - the newly turned Zerg - as a threat to their own plans for domination. Maybe a human general who once knew Percy and now wants to destroy him because he has joined the Zerg side.
There could be a group of poachers who are not just after regular game but are also involved in some dark magic. They oppose the hunters and especially Percy when he tries to stop their illegal and dangerous activities. They might have powerful backers or magic items that make them a formidable foe for Percy and the other hunters.
Perhaps it's one of Percy's former friends who has turned against him. This friend could be jealous of Percy's powers or has been influenced by some dark force. Their actions and taunts could be what drives Percy to become dark, making them the main antagonist in the story.
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 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.
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.