Madara Uchiha could still be the main antagonist even in a time - travel fanfiction. Imagine Naruto travels back to a time when Madara was still alive. Madara, being power - hungry as he is, would see Naruto's Six Paths powers as a threat and a tool he could use for his own ends. He would try to either steal Naruto's powers or manipulate him into doing things that would further his own goals of creating a world under his control.
Maybe an ancient demon that was once sealed by the Sage of the Six Paths but has now been released. This demon could be bent on revenge and see Naruto, as the inheritor of the Sage's power, as its main target. It would be a formidable foe, with abilities that could test Naruto's new - found powers and his resolve. The demon could also corrupt other ninjas to do its bidding, creating more chaos in the ninja world.
Maybe it's a corrupted spirit from the avatar world that has become jealous of Naruto's unique powers as the Sage of Six Paths. This spirit could try to possess Naruto or those close to him in order to gain access to his powers and use them to rule over both the Naruto and avatar universes. It would be a very powerful and menacing antagonist as it can manipulate the elements in the avatar world and has knowledge of Naruto's world through its research on him.
Perhaps an ancient demon that was sealed away by the original Sage of Six Paths is reawakening. This demon, having been dormant for so long, is extremely powerful and wants revenge on the world that the Sage of Six Paths helped create. It would see Naruto, as the reborn Sage, as the main obstacle in its path of destruction.
It could be Voldemort still. Even with Harry having the powers of the Sage of Six Paths, Voldemort would be a formidable foe. He might be intrigued by this new power and try to steal it for himself.
Kaguya could be a great antagonist. Even though she was sealed away, in a fanfiction, she could break free and seek revenge. Her power level is extremely high, and she has a deep understanding of the Sage of Six Paths Senjutsu, which would make her a formidable foe for Naruto.
A good antagonist could be a rogue ninja who has somehow managed to gain some of the power of the Otsutsuki clan. He wants to use the fem Sage of Six Paths' connection to the origin of chakra to open a gateway to a world full of power that he can rule. He sees Naruto and the Sage as threats to his plan and constantly tries to sabotage their efforts to protect the world.
Another possibility is a group of powerful ninja from a hidden village that has always been in the shadows. They view Naruto's power as a disruption to the balance of power in the ninja world. They would be the main antagonist as they try to undermine Naruto's rule as the God of Ten Paths, using all kinds of underhanded tactics, from assassinations to spreading false rumors to turn the other villages against Naruto.
Danzo could be a great antagonist. If Kakashi travels back in time, Danzo's underhanded plans, like his control over Root and his desire for power, would still be in motion. He'd likely oppose Kakashi's attempts to change things for the better, especially if it threatened his own influence.
Danzo could be a great antagonist. If Naruto travels back in time, Danzo's schemes and thirst for power would still be there. He might see Naruto as a threat to his plans of controlling Konoha and try to eliminate him. His underhanded methods and shadowy operations would make him a formidable foe for Naruto, especially when Naruto is trying to change the past for the better.
One potential main antagonist could be an older, power - hungry shinobi who has infiltrated the Anbu in the past. This shinobi could be jealous of Naruto's sudden rise in the Anbu (due to his future knowledge) and sees him as a threat. He then starts to plot against Naruto and the Anbu's new - found positive direction. Or perhaps it's a corrupt politician in the village who uses the Anbu as a tool and doesn't want Naruto to change the Anbu's loyalty from him to the village as a whole.