Maybe there's a powerful sorcerer who wants to use the cat girl's unique cat - human hybrid nature for his dark magic experiments. This sorcerer would be a great antagonist as he would constantly send his minions to try and capture the cat girl from Naruto. He could also be a threat to the entire village as his power grows with the potential use of the cat girl's abilities.
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.
There could be a rival village that discovers the cat girl and believes she can be used to gain an advantage over Naruto's village. Their leader might send their best warriors to try and steal the cat girl away. This would create a lot of conflict not only between Naruto and the rival village but also within Naruto's own village as they debate how to handle the situation to protect the cat girl and themselves.
Well, perhaps Naruto finds the cat girl alone and injured. He decides to take her in out of his kind heart. She might start to learn ninja skills from Naruto and his friends, and there could be a lot of comical moments as she tries to adapt to the human world while still having her cat - like behaviors.
It could be Orochimaru from the Naruto universe. He might be interested in the cat's special abilities, perhaps thinking he can use them to gain more power or immortality. He would be a formidable antagonist as he has his snake - like powers and is very cunning.
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.
There could be a group of mean - spirited fairies. They see Sakura as an intruder in their territory, which might be a beautiful garden that Sakura often visits. To drive her away, they use their fairy magic to turn her into a cat, thinking that she will be less of a threat in that form. And they keep thwarting her attempts to turn back into a human throughout the fanfic.
It could be an evil scientist who wants to capture the cat girl for her unique abilities. Maybe he wants to use her enhanced senses or agility for his own malicious purposes.
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.
The child could be an orphan from a small, destroyed village that Naruto comes across during one of his missions. This child might have lost their family to a powerful enemy and Naruto feels a sense of responsibility to take them in.
It could be a character who is jealous of the relationship between Roy and Edward. Maybe someone who wanted to adopt Edward themselves or has a grudge against Roy for taking Edward in.
Darkseid could be a potential main antagonist. He might view Superboy as a weapon that he wants to control. If he realizes that Batman is trying to shape Superboy into a hero of Earth, he would surely try to stop it. He could send his minions to attack Batman and Superboy or try to corrupt Superboy's mind from afar with his Omega Beams.