The Akatsuki might also be the main antagonists. They are a group of powerful and dangerous ninjas. Their goal of collecting all the tailed beasts would put Naruto in danger, and thus the fem Kyuubi would need to protect him from the likes of Itachi, Kisame and the other Akatsuki members.
It could be Orochimaru. He's always been after power and Naruto's unique abilities would be very appealing to him. So the fem Kyuubi would have to constantly be on guard against Orochimaru's schemes.
Another possibility is a new and powerful enemy from a neighboring village. This enemy might view fem Naruto as a symbol of the strength of her village and wants to take her out to weaken the village. Shikamaru then has to protect her from this external threat.
Perhaps there are some shinobi within the village who are jealous of Naruto's potential. They might try to harm Naruto in secret, and Hiruzen has to be vigilant against them. These shinobi could be from clans that have rivalries with the Uzumaki or those who just don't want a new powerful force emerging in the village.
Often, it could be the Akatsuki. They are always after the power of the tailed beasts, and with Naruto being protected by the Kyuubi, they would be major antagonists. They might come up with new and devious plans to try and get to the Kyuubi within Naruto.
Often, the Akatsuki still remain as main antagonists. Since Naruto's fusion with the Kyuubi makes him more powerful, they would be even more interested in capturing him for his power.
In this fanfiction, perhaps the fem Kyuubi protects Naruto by leading him to hidden places in the forest that are safe from the reach of his foes. She might use her knowledge of the area, which she has gained over the years of being in the Naruto world, to find these secret spots. And along the way, she could also teach Naruto some new skills or give him insights about his own powers that he hadn't considered before.
Another potential antagonist could be an inner demon within Naruto that is a manifestation of the Kyuubi's corruption. This inner demon could constantly be battling Naruto's good side, trying to take over completely. And there could be characters who misunderstand Naruto's situation and side with the forces that are trying to 'contain' or 'destroy' Naruto because they believe he is a lost cause due to the Kyuubi's corruption.
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 Akatsuki could still be the main antagonists. Even though Naruto has accepted the Kyuubi, they might see his new power as a greater threat or a valuable asset to capture. They could try to take the Kyuubi from Naruto to use for their own evil purposes.
Maybe some of Tony's business rivals who have access to advanced technology. They could be jealous of Tony's relationship with Ultron and try to harm him. They might hire mercenaries or develop their own weapons to go after Tony. In this fanfiction, these rivals would be the main antagonists as they constantly try to break through Ultron's protection of Tony.
In many cases, the main antagonists can be other Slytherins who still hold grudges against Harry or are loyal to the pure - blood supremacist ideology. They might see Harry as a threat to their way of life. Also, some Death Eaters can be antagonists. They target Harry because of his role in Voldemort's downfall and would stop at nothing to get to him.