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.
It could be a rogue group of ninjas who believe that the Sage of the Six Paths' power should not be in Naruto's hands. They form an alliance and try to steal the power from Naruto, believing that they can use it for their own purposes, which might include ruling the ninja world with an iron fist or selling the power to the highest bidder. They would use all kinds of underhanded tactics to achieve their goal, making them a complex and dangerous antagonist.
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.
One possible main antagonist could be a power - hungry ninja who wants to use Naruto's connection to the Sage of Six Paths for their own evil purposes. They might try to kidnap Naruto to extract the secrets from him.
In this fanfiction, the main antagonists could be a secret organization that has been studying the Six Paths powers in the shadows. They see Naruto as a threat to their plans of world domination. They could have their own powerful members with unique abilities that are specifically designed to counter Naruto's newfound powers as the Sage of the Six Paths. They might try to manipulate events and turn Naruto's friends against him to weaken his position.
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.
Yes, in some fanfictions, Naruto is depicted as the Sage of the Six Paths. Fanfiction writers often like to create alternate storylines where Naruto attains this powerful status. It gives them the freedom to explore different aspects of Naruto's character and the Naruto universe in a new and exciting way.
It could be a new character entirely. Maybe a young ninja who discovers they are the reincarnation. This would give the writer a lot of freedom to develop the character's growth and personality as they come to terms with their new identity.