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 main antagonists can vary widely. It could be that Orochimaru, still alive and more devious than ever, sees Naruto's fusion as an opportunity to gain the Kyuubi's power for himself. He might plot and scheme to get close to Naruto and somehow extract the Kyuubi's power. Or perhaps there are dark forces from outside the ninja villages that are awakened by the news of Naruto's fusion and decide to invade, seeing the now - more - powerful Naruto as the key to their conquest.
In some fanfictions, new antagonists might emerge. Maybe there are other hidden groups who fear the power of Naruto and the Kyuubi combined. They could be ancient clans or secret organizations that see this fusion as a threat to their own plans or power structures. Another possible antagonist could be a rogue ninja who has a personal vendetta against the Kyuubi and thus targets Naruto after the fusion.
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.
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.
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 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.
Sasuke could potentially be an antagonist. Even though they were friends before, Sasuke might see Naruto's new fused power as a threat to his own goals or ideals. He could challenge Naruto, thinking that Naruto's power is getting out of hand. Another could be some remnants of the Akatsuki. They might be interested in Naruto's new power and try to either steal it or use it for their own evil purposes.
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, in some 'naruto fused with kyuubi fanfiction', a cool plot point is that Naruto can communicate with the Kyuubi on a deeper level. They might work together to develop new and unique techniques. Also, the fusion could make Naruto a target for more powerful enemies who see him as a greater threat.
Maybe it would be a combined form of some of Naruto and Goku's most powerful enemies. For example, if Frieza and Orochimaru somehow combined their powers and knowledge. They would be a very tricky opponent for the fused Naruto - Goku as they would know the strengths and weaknesses of both heroes.