It could be an older version of Orochimaru who has found a way to manipulate time as well. He might try to stop Naruto from changing the past in a way that would undo his own evil plans in the future.
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.
Madara Uchiha could also be a main antagonist. If Naruto goes back to a time when Madara was still alive and plotting, Madara would surely oppose Naruto's attempts to change the future. He has his own grand plans for the world and wouldn't let Naruto interfere easily.
It could be Orochimaru. Imagine Orochimaru discovers baby Naruto's time - traveling ability and wants to use it for his own evil purposes. He might try to manipulate baby Naruto to change the timeline in a way that benefits him, like making it easier for him to gain more power or revive his dead comrades.
It could be a future version of Orochimaru who has found a way to come back even more powerful. Maybe he has developed some new form of immortality and is causing chaos in the future world that Naruto travels to.
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 Orochimaru from an earlier time. Since he was always after power and secrets, Naruto's knowledge of the Rasen Shuriken and his time - traveling abilities would be a huge threat to Orochimaru's plans. Orochimaru might try to steal Naruto's jutsu or use him to gain more power.
It could be a time - traveling villain from the future who wants to change the past to gain more power in their own time. They might try to stop Naruino from achieving their time - travel goals.
It could be an alternate - version of Tony Stark from a different timeline who has gone rogue. This version might have different values due to the differences in his timeline's history and is now causing problems in the main Stark's timeline.