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 possible plot could be that Naruto's mini Kyuubi form is initially out of control. He might accidentally attack the village when he was a child. But then, through the help of Iruka and Kakashi, he starts to learn to control this power. They teach him chakra control techniques specifically designed for his unique situation.
Iruka could still be an important ally. Even though Naruto's situation is different, Iruka would probably be drawn to his positive attitude. And the Third Hokage would also be on his side. He was always looking out for Naruto in the original story, and that would likely continue. Plus, any of the ninja who were friends with Minato would probably be friendly towards Naruto as well.
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.
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.
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.
The old - fashioned and conservative gods who don't like the idea of a new, young god like Percy shaking up their established order could be antagonists. They might see him as a threat to their power and try to undermine him.