Danzo could still be a major antagonist. Even if Naruto travels back in time, Danzo's thirst for power and his underhanded methods would still pose a threat. Naruto would have to find a way to deal with him without causing too much chaos in the village.
Orochimaru would also be a likely antagonist. Since he has his own evil plans in the original timeline, Naruto going back in time wouldn't necessarily change his motives. Naruto would need to use his knowledge to outwit Orochimaru and stop his experiments and plans for immortality.
It could be a time - traveling version of Zeref. He might be trying to stop Natsu from changing things in the past that could potentially lead to his own downfall in the future.
It could be a time - traveling pirate who has his own evil plans for the past. He might be trying to change the past to gain ultimate power in the future. So he becomes an obstacle for Luffy who wants to either preserve the past or make positive changes.
It could still be Orochimaru. Even if Sasuke travels back in time, Orochimaru's thirst for power and knowledge wouldn't change. He would still be plotting to gain power, and Sasuke, with his knowledge of Orochimaru's future actions, would be in a position to stop him. Orochimaru's experiments and his desire to take over the bodies of others make him a formidable antagonist.
In some cases, the antagonist could be Esme herself, or rather a version of her from the past. The past Esme might be more naive or self - centered and not understand the implications of Esme's actions in the past. The present Esme is trying to make positive changes, but the past version of herself keeps getting in the way, either through her own actions or by influencing the people around her in a negative way.
Aizen could still be the main antagonist. Even if Ichigo travels back in time, Aizen's long - term plans might be already in motion. Ichigo would have to find a way to expose and stop Aizen earlier than in the original timeline.
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 a new villain who has emerged during Naruto's absence. This person might be after the power that Naruto holds or wants to destroy the Hidden Leaf Village for some unknown reason.
It could be Orochimaru. Since Orochimaru has always been interested in power and immortality, if Naruto goes back in time, Orochimaru might sense the change in the timeline and try to stop Naruto from changing things that could affect his future plans for power.
Cell could be a great antagonist. Even if Gohan goes back in time, Cell might still find a way to exist. Maybe he adapts his plan to absorb the Androids earlier in time. Gohan would then have to face a more powerful and unpredictable Cell, who could potentially change the timeline to his own advantage.
Frieza would be a great antagonist. If Goku goes back in time to a point before Frieza was defeated, Frieza could be an even more menacing force as Goku might not have all the power - ups he had in the original timeline. He'd have to rely on his wits and basic training more.