Often, Orochimaru can still be a main antagonist. Even in a time - travel scenario, his thirst for power and immortality doesn't change. He might oppose Naruto and Tsunade's attempts to change the past as it could disrupt his own plans for power.
Madara Uchiha could also be an antagonist. If Naruto and Tsunade are trying to prevent the Uchiha massacre or change the future in a way that goes against Madara's long - term goals, he would surely fight against them. His powerful jutsu and strategic mind make him a formidable foe in any time period.
In some cases, the Akatsuki as a whole could be antagonists. Their goal of collecting all the tailed beasts might be at odds with what Naruto and Tsunade are trying to achieve in the past - travel plot. They would try to stop Naruto and Tsunade from changing things that could potentially prevent them from getting the tailed beasts.
Often, Orochimaru can be a main antagonist. Since he has his own devious plans in the Naruto universe, in a time - travel scenario, he might oppose Naruto and Tsunade's attempts to change things for the better. He could be trying to use the time - travel chaos to his own advantage, like stealing forbidden jutsu from different eras.
Often, it could be the same antagonists from the original Naruto series but in a different context. For example, Orochimaru might still be an antagonist if he tries to use the time - travel situation to his advantage, like getting his hands on some ancient forbidden jutsu.
In some versions, Orochimaru could be a main antagonist. Since he has his own devious plans and is always looking for power, Naruto and Ino might have to deal with him all over again as they travel back in time. He could be trying to interfere with their attempts to change the past.
It could be a group of rogue ninjas who also ended up on the island. They might be after some valuable resource on the island and see Naruto and Tsunade as obstacles.
It could be a group of rogue ninjas who want to steal Naruto's godlike powers for themselves. They might be led by a powerful and evil ninja who has his own motives for wanting such power.
It really depends on the specific fanfiction. However, it could be that they travel back to a time when Orochimaru was at his most devious, so he would be a main antagonist. His experiments and thirst for power could pose a great threat to Naruto and Shikamaru's mission in the past.
It could be some of the historical villains from Naruto's past that were thought to be long gone but are now resurfacing due to the time travel. For example, Madara Uchiha might be an antagonist if they travel back to a time when he was still active and plotting against Konoha.
It could be the same antagonists from the original Naruto series, like Orochimaru or Madara Uchiha. Since Naruto and Temari are time - traveling, they might encounter a younger version of these villains at a time when they were just starting their evil plans. Another possibility is that they create new antagonists by changing the past in some way. For example, if they prevent a certain character from dying, that character could turn out to be an antagonist in the altered timeline.
One possible main antagonist could be Madara Uchiha from an earlier time period. If Naruto and Kyshina travel back far enough, they might encounter a younger and more power - hungry Madara. He could be a major obstacle as he tries to achieve his early goals of creating a world under his control, which would be in direct opposition to what Naruto and Kyshina are trying to do to protect the future of the village.
One potential antagonist could be Orochimaru. If Naruto and Temari travel back to a time when Orochimaru was at the height of his power and evil plans, he would surely oppose them. He might see their knowledge of the future as a threat to his schemes to gain immortality and power over the ninja world.