It could be a relative of one of Naruto's old foes. For example, a nephew of Orochimaru who has been taught by Orochimaru's remaining followers. He might be jealous of the peace Naruto has brought and wants to disrupt it by targeting his kid.
Maybe a new ninja from another village who believes that Naruto's kid has some sort of power that could be a threat to his own village in the future. So, he decides to be the main antagonist and try to eliminate the kid before he grows too powerful. This would set up a conflict not just between individuals but also between villages in the fanfiction.
It could be a bully in the village. This bully could constantly pick on Naruto because of his status as the Jinchuriki of the Nine - Tails. He might try to steal Naruto's food or prevent him from playing with other kids.
Perhaps a long - lost relative of Voldemort who has been in hiding all these years. This relative has discovered a way to gain power through Harry's kid. They might start by infiltrating Hogwarts under a false identity and slowly manipulate events to get closer to the kid. Their ultimate goal could be to sacrifice the kid in a dark ritual to bring back the dark days of Voldemort's reign.
It could be a powerful ninja who wants to capture the fox brother for his own purposes. Maybe he believes that the fox brother's powers can be used to take over the ninja world. This antagonist might be from a rival village or a secret organization within Naruto's own village.
It could be Orochimaru. He is always interested in new and powerful weapons. With Naruto having hidden blades, Orochimaru might see it as a threat and try to take the blades for himself, leading to a conflict.
It could be a rogue ninja who was once part of the same clan that the hidden blade belongs to. He wants the blade back to gain ultimate power and is willing to do anything to get it from Naruto.
It could be a rogue ninja who also has a rare bloodline and sees Naruto as a threat to his own power and status. This antagonist might want to steal Naruto's bloodline or simply eliminate him to be the only one with such a special ability.
Perhaps the main antagonist is a dark figure from within Konoha itself. This person doesn't want Naruto's family to be reunited because it could expose some dark secrets about their own actions in the past. They would do anything to keep the sister hidden and Naruto in the dark, even if it means causing harm to both of them.
The Reverse - Flash would be a great antagonist. His time - traveling abilities and his vendetta against the Flash family could make for a really intense story, especially if he teams up with other villains from the Kid Flash's universe in a crossover.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
The Green Goblin could be a great antagonist even when Peter is just a kid. He could be starting out his evil deeds in a more low - key way that still catches Peter's attention. Maybe he's stealing from small businesses in Peter's neighborhood, and Peter starts to suspect something is up.