There could be a new villain created just for this fanfiction. Maybe a scientist from a secret organization who wants to study Ben 10 in his new form. This villain could try to capture Ben 10 and perform all kinds of experiments on him, seeing his transformation as a unique opportunity to learn more about the Omnitrix and its capabilities.
It could be Vilgax. He might see Ben 10's new form as a weakness and try to take advantage of it.
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.
Hex could also be a main antagonist. He might be jealous of the Lucky Girl's natural powers and try to corrupt her or use her powers for his own evil magic. He could set up traps and illusions to try and capture her, and also try to turn Ben against her so he can deal with them separately.
The main antagonist could be an alien who has a vendetta against Ben specifically. This alien might be able to sense Ben's true identity even when he's dressed as a girl. He could try to expose Ben and foil his mission or just cause general chaos while Ben is in his disguised state.
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 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.
Maybe a malevolent scientist who has a grudge against female heroes. He believes that only men should have such powers and sets out to take the Omnitrix from Ben and use it for his own evil purposes. He underestimates Ben because she is a girl but soon realizes his mistake.
Another possible antagonist could be an alien scientist who was involved in the creation or discovery of the Necrofriggian babies. This scientist might have his own evil plans for the babies and sees Ben as an obstacle in his way. He could be using his advanced technology to try and capture the babies from Ben.
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.
It could be Vilgax. He might see the chaos caused by the monster girl transformations as an opportunity to finally defeat Ben. He could try to use the monster girls' new powers against Ben or even find a way to control them to do his bidding.
Perhaps a half - alien, half - vampire hybrid. This character was shunned by both species and blames Ben for making him feel even more like an outcast. He uses his unique powers to create chaos and tries to turn Ben into a vampire - alien like himself.