Maybe an alternate version of Natsu himself from a different timeline. This 'evil Natsu' could be trying to prevent the 'good Natsu' from making positive changes in the past, as it would disrupt his own plans for domination in his timeline.
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.
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.
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.
It could be Zeref. If Natsu goes back in time, Zeref might have different plans or be in a more powerful position at that time. He could be the main obstacle for Natsu to overcome, especially if Natsu is trying to change things related to the dark magic that Zeref wields.
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.
Another option could be a dark wizard from the past who was once defeated by the founders of Fairy Tail. But Natsu's time - traveling causes some sort of ripple effect that brings this wizard back to power. He then wants to take revenge on the guild and sees Natsu as a symbol of the future that he wants to destroy.
It could be a dark mage from the past who was sealed away but gets released because of Natsu's time travel. Maybe a mage who was trying to conquer the world back then and now sees Natsu as a threat to his new plans. Another option is a time - traveling villain who is trying to change history for his own evil purposes and Natsu has to stop him.
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.