It could be a rogue ninja who was once rejected from the lightning sage training and now wants to destroy the entire concept of the lightning sage. He might have developed his own dark lightning - based techniques to oppose the traditional ones.
A powerful and corrupt ninja lord from a rival village could be the main antagonist. He sees the emerging lightning sage as a threat to his plans of domination. So, he sets out to either capture or kill the lightning sage. He might have a group of highly skilled ninjas under his command, and he could also be in possession of some powerful anti - lightning - sage artifacts or jutsus that he uses to try and stop the lightning sage at every turn.
Perhaps an ancient demon that was sealed by the Star Sage long ago has now broken free and is seeking revenge. It sees the descendants of the Star Sage as a threat and tries to eliminate them one by one. The main characters then have to find a way to defeat this demon using the limited knowledge they have about the Star Sage.
It could be a rogue ninja from a hidden village who has also mastered lightning jutsu and wants to prove himself stronger than Naruto. This ninja might have a personal vendetta against Naruto or Konoha.
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.
It could be a power - hungry shinobi within Kiri. This shinobi might see the Sage as a threat to his own rise in the village hierarchy. So, he uses his influence to keep the Sage neglected and also tries to sabotage any attempts by the Sage to gain recognition.
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.
A rogue ninja from a neighboring village who has also mastered a similar but dark - powered version of the Lightning Rasengan. He could be jealous of Naruto's fame and power and wants to prove that his version is superior.
It could be a rogue ninja who has also mastered lightning - based jutsu. This antagonist might be jealous of Naruto's growing power and fame, and wants to prove that his lightning skills are superior. So, he constantly challenges Naruto in battles where lightning jutsu are the main form of combat.
Another possibility is a dark wizard who has been secretly studying the power of the God of Lightning for years. This wizard wants the power all for himself and sees Harry as an obstacle. He could be a former Death Eater who has broken away from Voldemort's group to pursue this power on his own. He would use his knowledge of dark magic and his own minions to try and take the power from Harry.
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.