Sometimes, the main antagonists could be past versions of the Akatsuki members. If Naruto and Shikamaru travel back to a time when the Akatsuki was just forming or in the middle of their most dangerous operations, they would have to face off against the likes of Pain or Itachi (although Itachi's motives are complex). These powerful ninjas would be a huge obstacle for our time - traveling heroes.
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.
Well, it could be Orochimaru. Even if they travel in time, Orochimaru's thirst for power and knowledge might make him an antagonist. He could see Sasuke and Shikamaru as threats to his plans, especially if they are trying to change the past which might interfere with his own schemes.
Madara Uchiha could be an antagonist as well. Even if they travel back to a time before his grand plans were fully in motion, he would still be a very powerful and dangerous foe. He might sense that Naruto and Shikamaru are from the future and try to use their knowledge for his own purposes, or simply eliminate them if they stand in his way.
Another possibility is a new and powerful enemy from a neighboring village. This enemy might view fem Naruto as a symbol of the strength of her village and wants to take her out to weaken the village. Shikamaru then has to protect her from this external threat.
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.
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.
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 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.
Danzo Shimura might be another one. He is very secretive and power - hungry. If Naruto and Naruko's time - traveling actions expose his dark deeds or interfere with his control over the village, he would become their enemy. He has many underhanded methods and a strong influence within the village that they would have to deal with.