Perhaps the main antagonist could be a group of ninja from a long - forgotten village that resurfaces during the time skip. They have a grudge against the major ninja villages like Konoha, and they want to reclaim what they believe was stolen from them in the past. They could have unique and dangerous fighting styles that the main characters have never seen before.
It could be a rogue ninja who has mastered a forbidden jutsu during the time skip. This ninja might have been a former ally or a student from one of the ninja academies who turned to the dark side. His goal could be to take over all the ninja villages using the power of the forbidden jutsu.
The main antagonist in a 'naruto time skip fanfic' could be an ancient spirit that was accidentally released during some sort of experiment during the time skip. This spirit is bent on destruction and chaos, and it uses its ability to possess other ninjas to cause mayhem. Naruto and his friends would have to find a way to exorcise the spirit before it's too late.
There's also the possibility of a new, unknown threat emerging from a different dimension or realm. This antagonist could be a powerful being with abilities that the ninja world has never seen before. He sees Naruto's newfound power as a threat to his own plans of conquest and decides to target him first, leading to a series of epic battles across different locations in the Naruto universe.
It could be Orochimaru. Since Orochimaru has always been interested in power and immortality, if Naruto goes back in time, Orochimaru might sense the change in the timeline and try to stop Naruto from changing things that could affect his future plans for power.
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.
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 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.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
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.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.