A new group of rogue ninjas who oppose the idea of a female Hokage could be antagonists. They could be made up of traditionalist ninjas who believe only men should hold power. They would constantly try to undermine the female Naruto's progress, whether it's by attacking her directly or spreading rumors to turn the village against her.
The Akatsuki could be great antagonists as always. But in this AU, they might target the female Naruto specifically because of her potential to change the ninja world in a different way. They could see her as a threat to their plans, especially if she's advocating for more equality among ninjas, which could disrupt the power balance they're trying to achieve.
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.