A powerful and secret organization that has its own plans for the ninja world could also be an antagonist. They see the child of prophecy as a threat to their long - term plans. They might send their best assassins or use dark jutsu to try and stop the child. They could also try to corrupt the child, turning them to the dark side, so that they can use the child's power for their own evil purposes.
Another antagonist could be a group within the ninja village itself. Maybe they fear the changes that the child of prophecy might bring. They could be the more conservative elements who don't want to see new ideas or powers emerging. They might try to undermine the child's training or spread false rumors about them. For example, they could claim that the child is a danger to the village, turning public opinion against the child.
Iruka could be a potential ally. He has always had a bit of a soft spot for Naruto. Even in the face of Naruto being neglected, Iruka might step up more and offer more than just basic support. Another could be Shikamaru. He is smart and might see the value in Naruto that others are missing. He could help Naruto strategize to get out of his neglected situation.
It could be a new character created by the author. Maybe someone who was born in a small, overlooked part of the village and has a power that is related to the prophecy but has been dormant until now.
A group of rogue ninjas who have made the island their base could be antagonists. They might see Naruto as a threat to their operations on the island.
Orochimaru could still be an antagonist. He might see Naruto as a threat especially if Kakashi is training him intensively. His goal of obtaining power could lead him to target Naruto.
The Otsutsuki clan members other than Kaguya could be antagonists. Since Kaguya is training Naruto, they might see Naruto as a threat to their plans.
A group of traditionalists in Akeno's world could be antagonists. They might not approve of the idea of a harem or of an outsider like Naruto having so much influence. So they could try to break up the harem and drive Naruto out of their world by using political means, like spreading false rumors about Naruto and his friends.
Perhaps a powerful and corrupt merchant group could be the antagonists. They are secretly trying to take over the village's economy and resources. They use bribes and blackmail to get their way. The Sixth Hokage discovers their plot and has to stop them without causing too much chaos in the village's economic system. They may also have some ninja mercenaries working for them.
Well, Hinata can be a common character paired with the child of prophecy. Given her gentle and kind nature, she might play a nurturing role. Shikamaru is another possibility. His intelligence could complement the child's abilities, and they could work together to solve various problems in the fanfiction. There are also cases where Orochimaru might be involved in a complex relationship with the child of prophecy, either as an adversary or an unexpected ally.
A former acquaintance of Beckett who has turned to a life of crime could be an antagonist. They might have some old grudge against Beckett, like Beckett once reported them for something minor but it led to them having a really hard time, so now they want revenge by holding Beckett hostage.
The established nobles who fear losing their power could be antagonists. They might try to plot against the new king to keep their old ways and privileges. Another potential antagonist could be a powerful and jealous rival who believes he should be the king instead.