There's also the possibility that the main antagonist is an outside force from another dimension or a powerful entity that was awakened in the future. This entity might see the ninja world as a threat or simply want to conquer it for its own gain. Naruto would need to figure out how to defeat this unknown and powerful foe during his time in the future.
It could be a future version of Orochimaru who has found a way to come back even more powerful. Maybe he has developed some new form of immortality and is causing chaos in the future world that Naruto travels to.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
It could be a future version of an existing villain who has also found a way to time - travel. For example, a more powerful and cunning Orochimaru from a future timeline where he has mastered even more dark jutsu. He might try to stop Naruto from changing the past in ways that would prevent his own rise to power.
It could be Orochimaru. Even in the academy days, he was already plotting and scheming. If Naruto time - travels back, Orochimaru might see him as a threat to his early plans and target him. Orochimaru's thirst for power and knowledge makes him a great antagonist for this scenario.
It could be a new character that Naruto discovers through reading the future. Maybe someone who has a grudge against the Hidden Leaf and is planning a huge attack in the future.
Cell could still be a great antagonist. Imagine a scenario where in the fanfiction, Cell follows Future Trunks through time. He then starts to absorb different beings in the new timeline in a more devious way than in the original story.
It could be a new character, perhaps someone from a far - off land who has a grudge against Naruto's future self for some reason. This character might be extremely powerful and has plans to destroy everything Naruto holds dear. When Naruto sees this future, he has to find a way to stop this new threat before it even begins to form.
A time - traveling pirate who has his own agenda and wants to change the course of pirate history for his own gain could be the antagonist. This pirate might be jealous of Luffy's future achievements and try to stop him from ever becoming the Pirate King by changing things in the past.
The Riddler could be a great main antagonist. He could use his knowledge of time paradoxes and puzzles to try and outwit Batman as he travels through time. He might set up elaborate traps across different time periods that Batman has to solve.
It could be a new character. Maybe someone who has been influenced by the dark side of the ninja arts and wants to overthrow the current order. This new antagonist might be jealous of Naruto's success and the peace in the village, and they strive to create chaos.