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.
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.
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.
It could be an evil ninja who has already made a pact with the Abyssal God and wants to use its power to take over the ninja world. He might see Naruto as a threat to his plans because Naruto has a natural connection to the god's power.
Maybe an ancient being that was sealed away long ago but has now been awakened due to Naruto's newfound power. This being has a natural hatred for those who can control lightning and sees Naruto as a threat to its plans of taking over the ninja world. It has the ability to manipulate shadows and uses them to counter Naruto's lightning attacks.
Perhaps an organization that views the 'god of illusions' as a threat to their plans for world domination. They might see the 'god's' influence over illusions as something that can disrupt their schemes. So they send their most powerful agents to take on the 'god of illusions'. This could lead to some epic battles in the fanfiction.
It could be an evil shinobi who has somehow managed to control or manipulate the God of Death's powers for his own malicious purposes. This shinobi might use the power to create chaos in the ninja world, like raising the dead and making them fight against the living.
It could be a rogue ninja who has also harnessed the power of a god of destruction. This ninja wants to use the power to rule the ninja world and Naruto has to stop him.
It could be a powerful ninja who is jealous of Naruto's new godly powers. He wants those powers for himself and will stop at nothing to get them.