Kabuto could also serve as the main antagonist. He is a sly character. He might enter the race with the intention of gathering data on all the participants, especially Naruto and his friends. He could use his medical ninjutsu to enhance his own racing abilities in unfair ways, like numbing pain to push himself further or using some sort of drug - like jutsu to boost his speed.
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.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.
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.
Madara Uchiha could be a great antagonist. His powerful Sharingan abilities and his grand plans for the Naruto world would put him at odds with Supergirl. He might see her as a threat to his control and try to manipulate or defeat her. Another option could be Kaguya Otsutsuki. Her god - like powers and desire to reshape the world would clash with Supergirl's values and her attempts to protect the people of the Naruto universe.
A powerful rogue ninja who wants to steal the Nanosuit from Naruto could be the main antagonist. This ninja might have his own reasons, like using the suit to take over the ninja world.
It could be one of the powerful Deadman characters who see Naruto as an intruder and a threat to their world.
It could be a new villain who has emerged during Naruto's absence. This person might be after the power that Naruto holds or wants to destroy the Hidden Leaf Village for some unknown reason.
It could be a rogue ninja from a hidden village that was thought to be extinct. This ninja has a vendetta against Konoha and targets Naruto specifically because of his status as a hero. He would constantly try to thwart Naruto's counterattacks and plans.
Perhaps a group of rogue ninjas who are threatened by Naruto's shapeshifting ability. They might see him as a threat to their plans and try to eliminate him. They could be led by a mastermind who is well - versed in countering shapeshifting techniques.
It could be someone who also wants the Darksaber for their own dark purposes. Maybe a rogue ninja who has heard of the saber's power and will stop at nothing to get it from Naruto.