It could be Orochimaru. Orochimaru is always interested in strange experiments and new forms of power. He might see Naruto in his female form as an interesting specimen to study or use for his own evil purposes.
The Akatsuki could also be the main antagonists. They might initially be confused by Naruto's new form but then see it as an opportunity. They could try to capture Naruto, thinking that as a girl, he might be easier to subdue or that his new form holds some kind of unique power that they can use for their plan to capture all the tailed beasts.
It could be an alien bounty hunter. This bounty hunter has been hired to capture Ben in his stuck - as - alien form. The hunter might have some special gadgets or powers that make it difficult for Ben to escape. And he's not interested in Ben's well - being, just in getting the reward for bringing him in.
It could be a group of rogue ninjas who are after the cat girl for some special power she might possess. They see Naruto as an obstacle in their way to get to her.
Maybe a mechanical tyrant in a steampunk - inspired setting. This tyrant has created an army of mechanical beasts and is trying to rule the city. Pyro, as a girl with fire powers, is the only one who can melt the metal parts of the beasts and stop the tyrant. The tyrant sees her as a threat to his rule and is constantly trying to eliminate her.
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.
Well, the plot could involve Naruto waking up one day in a female body. He might struggle to adapt to the new physical form at first. Maybe he has to deal with different reactions from his friends, like Sasuke being really confused. And he could face new challenges in his ninja training, as his body now has different capabilities and limitations compared to when he was male.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.