Another possibility is that an old enemy of the Uzumaki clan resurfaces. They use Itachi's complex relationship with the village and his own motives to manipulate him into kidnapping fem Naruto. So, this old enemy would be the main antagonist as they are the ones driving the overall conflict.
Itachi himself could be seen as the main antagonist in this scenario. After all, he is the one doing the kidnapping.
Well, in this fanfiction, perhaps Itachi is being manipulated by some dark force. He kidnaps fem Naruto because he's under the control of this force which thinks that Naruto, being female in this version, holds the key to some sort of ancient prophecy. Itachi is then in a struggle between his loyalty to the village and the commands of this dark entity.
Prussia would likely be the main antagonist in this scenario since he is the one carrying out the kidnapping. His actions are against Fem Canada's will, which makes him the opposing force in the story.
Itachi himself could be seen as the main antagonist in this scenario as he is the one carrying out the kidnapping. He is acting against Sakura's will and causing a dangerous situation for her.
It could be Orochimaru. He might have manipulated Kushina into kidnapping Naruto. Orochimaru has always been interested in the power of the Uzumaki clan and Naruto's nine - tailed fox power. He could be using Kushina as a tool to get to Naruto.
It could be a rogue ninja who has a vendetta against the Hidden Leaf Village and specifically targets Naruto and Fem Katsuyu because of their unique partnership. This ninja might have some dark jutsu that can counter Fem Katsuyu's abilities.
It could be Orochimaru. Since he's always after power and Naruto, with Itachi's training, would become a more appealing target. Orochimaru might see Naruto as a threat to his plans of obtaining all the jutsu in the ninja world.
Itachi himself could be seen as the main antagonist in this scenario as he is the one performing the kidnapping. His actions are against Sakura's will and are likely to cause distress and conflict.
Obviously, the fem Kyuubi herself could be the main antagonist. Since she is the one manipulating Naruto, her actions are causing problems and driving the conflict in the story.
It could be an evil ninja who wants to capture the fem Kyuubi for her power. He might see the unique bond between Naruto and the fem Kyuubi as a threat to his plans of world domination.