It's also possible that a new antagonist could be created within the context of the time - travel. Maybe someone from the future follows them back in time and tries to stop them from changing things because they want to preserve the original timeline for their own selfish reasons. This new character would then become a major obstacle for Naruto and Ino to overcome.
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.
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, 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.
It could be the same antagonists as in the original Naruto series at first, like the Akatsuki. But if Naruto and Ino change things, new antagonists might emerge. Maybe some ninja who were once allies turn against them because they fear the changes Naruto and Ino are making to the ninja world order.
Often, it could be rogue ninjas. They might target Ino because of her family's importance in the village, and Naruto gets forced into protecting her. These rogues can be after some secret technique that Ino's family guards. Another antagonist could be a power - hungry shinobi from another village who wants to use Ino as a pawn to gain leverage over Konoha. Naruto then has to step in and stop them.
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.
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.
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.