A really interesting antagonist could be a mysterious figure from a hidden organization. This person has been secretly observing Naruto's family for a long time. They have a master plan that involves using Naruto's daughter as a key component. Maybe they want to use her unique chakra or abilities for some dark purpose. They would be constantly manipulating events behind the scenes, setting up traps and challenges for her, all while remaining in the shadows, which would make them a very menacing and unpredictable foe.
One possible group of antagonists could be those in the Hidden Leaf Village who still hold a grudge against the Kyuubi. They might see the daughter as a threat and try to get rid of her. Another could be rival villages that fear the power she might possess and see her as a weapon that could be used against them in the future, so they would try to eliminate her before she becomes too powerful.
The Joker would be a classic choice. His chaotic and unpredictable nature would pose a great threat to Batman's daughter. He might try to corrupt her or use her as a pawn in his evil schemes against Batman.
It could be a new group of rogue ninjas who oppose the ideals of the Hidden Leaf Village. They might target Kakashi's daughter because of her connection to Kakashi and Naruto, seeing her as a symbol of the village's new generation of strength.
The Titans could be great antagonists. They might see the daughter of Hecate as a threat to their plans of taking over. Her magic could be something they want to either control or destroy.
A rogue slayer who has turned to the dark side. She might envy Buffy's daughter's connection to Buffy and the legacy she represents. This rogue slayer could be using her powers for evil, like causing chaos in the human world and trying to eliminate any competition, which includes Buffy's daughter.
It could be a group of dark wizards who are jealous of Harry's status and see Lemon as a way to get to him. They might try to kidnap her or manipulate her to get Harry to do their bidding.
The main antagonists could be those who envy her wisdom. They might be jealous of the attention she gets or the power that her wisdom gives her. So, they try to undermine her at every turn, spreading false rumors about her or trying to make her look foolish in front of important people.
The Penguin could be a great antagonist. He might see Batman's daughter as a new threat to his criminal activities in Gotham. He could try to set traps for her, using his devious mind and his army of thugs.
Sasuke could still be an antagonist in a way. Maybe in this AU, he's more dismissive of the female Naruto because of his own ideas about strength and gender. He might see her as weak at first and that could create a lot of tension between them.
It could be some rogue ninjas who are after Lemon for some reason. Maybe they think she has a special power that they can use for their evil plans.