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.
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.
Obviously Naruto and the fem Kyuubi would be the main characters. Naruto is the one being corrupted and the fem Kyuubi is the one causing the corruption.
The Akatsuki could still be the main antagonists. Even with Naruto's training by the Kyuubi, they would be after the tailed beasts. Their goals of collecting all the tailed beasts would put them in direct conflict with Naruto. And they have some really powerful members like Pain and Itachi.
The main antagonists could be the villagers who fear Naruto's mini Kyuubi form and try to drive him out of the village. Their prejudice and fear act as a major obstacle for Naruto, who just wants to be accepted.
Well, one possibility could be that the female Kyuubi's influence changes Naruto's personality. Maybe she makes him more aggressive or self - centered in the fanfiction.
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.
One possible plotline could be Naruto gradually losing control over his own actions as the Kyuubi's influence grows stronger. For example, he might start to act more aggressively towards his friends without realizing it.