It could be a group of rogue ninja who are after the Uzumaki's powerful sealing jutsu. They see it as a way to gain unlimited power and rule the ninja world, so they target the Uzumaki clan, which makes Naruto their main enemy as he stands in their way.
Maybe a hidden organization that has a vendetta against the Uzumaki for some past event. They believe that by destroying the Uzumaki clan, they can rewrite the history of the ninja world in their favor. Naruto has to fight them to protect his clan and the legacy of the Uzumaki.
Perhaps an old enemy of the Uzumaki clan, long thought to be defeated, resurfaces. They see Naruto as a threat because of his position as the heir and aim to eliminate him before he can fully embrace his Uzumaki heritage and power. This could be someone with a vendetta against the Uzumaki for past events, like a clan that was defeated by the Uzumaki in the past and now wants revenge.
Well, perhaps the Uzumaki clan's secrets are being targeted. Naruto finds out that there are people after the Uzumaki's sealing techniques. He steps up to fight because he realizes the importance of his clan's legacy. He starts by training harder to master any Uzumaki - related powers he hasn't fully grasped yet. Then he embarks on a journey to find the source of the threat and take them on, all while trying to uphold the honor of the Uzumaki clan.
The Akatsuki could also be antagonists in Uzumaki clan revenge fanfiction. They were after powerful ninja and the Uzumaki clan was full of power. They could have been the ones who initiated the attack on the Uzumaki clan to get their hands on things like the Uzumaki's powerful chakra or their sealing techniques. And then there might be a secret group within the Leaf Village itself that was involved in the Uzumaki clan's downfall, perhaps out of fear of their growing influence.
Another potential antagonist could be a rogue shinobi who has a vendetta against the Uzumaki clan from the past. He doesn't want to see the clan restored and uses his own dark jutsu and a network of followers to try and stop Naruto at every turn. He might be jealous of the power the Uzumaki once held and fears they will regain that power.
The main antagonists could be a group of rogue ninjas who are after the secrets of the Uzumaki clan. Since Naruto is Mito's brother, they might target him to get to those secrets.
The main antagonists could be some of the conservative elders in the Hidden Leaf Village. They banished Naruto in the first place and would see his rebuilding of the Uzumaki clan as a threat to their power. They might try to undermine his efforts by spreading false rumors about him and his new clan.
Danzo could be a main antagonist. He was always paranoid about the Uchiha clan's power and was involved in many of the events that led to their downfall. In a fanfiction where Naruto is trying to save the clan, Danzo would likely oppose Naruto's efforts as he sees the Uchiha as a threat to his own power and the village's stability in his own twisted way.
It could be a group within Naruto's own clan who have turned against the rest of the clan due to some ideological differences. They might want to use the clan wars as an opportunity to take over the clan and change its values. Another possibility is a mysterious and powerful ninja from another land who has his own motives for causing chaos during the clan wars.
It could be a group of power - hungry humans who see the Laguz as a resource to be exploited. They might want to use the Laguz's unique abilities for their own gain, like using their strength in labor or their magical abilities for warfare.
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.