A dark version of one of Ben's own alien forms could be the antagonist. This dark form could be corrupted by an unknown force and turns against Ben. Since Ben is now a girl, this dark form might target her specifically, thinking she is easier to defeat, but Ben uses her unique qualities as a girl, like her intuition, to fight back.
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 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.
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.
Vilgax could be a great antagonist. He could hack into the gaming systems to try and defeat Ben in a virtual world where the rules are different. He might use his advanced technology to create digital versions of his minions to attack Ben.
It could be a new alien species that Ben has never encountered before. This species could be territorial and see Ben as a threat to their planet where he's stranded. They constantly try to drive him away or capture him, which makes it difficult for Ben to find a way to leave.
One option could be an alien scientist who is obsessed with the power of the Nemetrix. He wants to study it and use it to create his own super - weapons. He might be from a race that has been at odds with the creators of the Nemetrix for centuries.
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.
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.
Vilgax could be a great main antagonist. He has a long - standing feud with Ben and his appearance would immediately up the stakes. He could also manipulate Kevin into turning against Ben for a while.
Perhaps the main antagonist could be a former ally of Ben who has turned bad. After dawn, this character reveals their true intentions and starts causing trouble for Ben. They might have some sort of grudge against Ben or be power - hungry and see the Omnitrix as a means to gain ultimate power. They could use their knowledge of Ben's abilities and weaknesses to their advantage.