Maybe it's a human villain who runs an underground fashion empire and is using his business for evil purposes. Ben, dressed as a girl, infiltrates this fashion - related criminal organization. The villain becomes the main antagonist as he tries to stop Ben from uncovering his secrets and bringing him to justice.
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.
It could be Vilgax. He might see Ben 10's new form as a weakness and try to take advantage of it.
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.
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.
Perhaps a group of bandits could be the main antagonists. They spot Link dressed as a girl and think he's an easy mark. But when they realize that Link is actually a very capable fighter, they become determined to take him down. They start hunting Link, causing him to constantly be on the run and having to use his wits and skills to survive while still in his female disguise.
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.
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 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.
In this fanfiction, Ben could be part of a bet or a dare where he has to dress as a girl for a day. As he goes about his day dressed as a girl, he encounters various challenges. For example, he might have trouble using the girl - themed Omnitrix transformations because they behave differently when he's in female form. He also has to deal with the stares and comments from people around him, which makes for an interesting and comical story.
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.
An old enemy of the Omnitrix's creator could be a great main antagonist. Maybe this enemy was locked away for centuries and now has escaped and blames the Omnitrix for his imprisonment. He would be extremely powerful and have knowledge of the Omnitrix's weaknesses that Ben doesn't even know yet.