It could be the same antagonists as in the original Naruto series at first, like the Akatsuki. But if Naruto and Ino change things, new antagonists might emerge. Maybe some ninja who were once allies turn against them because they fear the changes Naruto and Ino are making to the ninja world order.
Perhaps Orochimaru, if he somehow discovers Ino's time - traveling. He has always been interested in power and forbidden jutsu. He might try to use Ino's ability for his own gain, and if she resists, he would become an antagonist. He could also try to stop her from changing things that he wants to keep as they are for his own evil purposes.
In some versions, Orochimaru could be a main antagonist. Since he has his own devious plans and is always looking for power, Naruto and Ino might have to deal with him all over again as they travel back in time. He could be trying to interfere with their attempts to change the past.
Often, it could be rogue ninjas. They might target Ino because of her family's importance in the village, and Naruto gets forced into protecting her. These rogues can be after some secret technique that Ino's family guards. Another antagonist could be a power - hungry shinobi from another village who wants to use Ino as a pawn to gain leverage over Konoha. Naruto then has to step in and stop them.
Well, they could also change their own relationships. Maybe Naruto wouldn't be so alone as a child, and Ino could become a stronger ninja earlier. They might train together in ways they didn't before, using the knowledge of future jutsu and strategies. They could also influence the relationships between different ninja clans, like improving the relations between the Uzumaki and the Yamanaka clans.
The Sith, of course. Even in the past, the Sith would be a major threat. They might try to stop Luke and Rey from changing things that would be detrimental to their plans for galactic domination.
It could be a new group of rogue ninjas who have a vendetta against Konoha. They might be led by a powerful and cunning ninja who has a personal grudge against Naruto or the village in general.
The main antagonists could be the original Naruto's friends and allies. Since this is an evil Naruto, people like Sasuke, Sakura, and Kakashi would likely oppose him and try to stop him from whatever evil plans he has in the past.
In some cases, it could be other time - traveling vampires or supernatural beings who have their own agendas. They might not want Bella to interfere with the past as it could disrupt their own plans or power bases. These antagonists could be more shadowy figures, working behind the scenes to thwart Bella's efforts.
Team Rocket could still be antagonists. Even if Ash goes back in time, they might be up to their old tricks of trying to steal Pokémon. Only this time, Ash has the advantage of knowing their future plans and can thwart them more easily.
It could be the village elders. They often have a lot of power and influence in the Naruto universe. If they believe Naruto is a potential threat or they have some ulterior motives, they could be the ones holding him back, thus acting as antagonists.