Another possibility is that the antagonists could be the very people they are trying to help. If their actions in the past are misinterpreted, the local ninja or villagers might see them as a threat and try to stop them. This would create an interesting dynamic where Naruto and Tenten have to not only deal with the actual threats but also with the misunderstandings of the people around them.
Maybe some of the historical villains who were thought to be dead. If Naruto and Tenten's time travel disrupts the natural flow of time, it could bring back villains like Orochimaru in his prime or some ancient evil ninja clans that were long forgotten. They would see Naruto and Tenten as threats to their re - emerging power.
One possible antagonist could be a rogue ninja from another village. They might target Tenten for her unique weapon - handling skills, thinking they can use her to create powerful weapons for themselves. Naruto would then have to face this ninja to save Tenten.
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.
It could be rogue ninja from a hidden village. They might be after Tenten because she has some sort of valuable information or a powerful weapon in her possession. Naruto gets in their way to protect her, and these rogue ninja use their forbidden jutsus to overpower Naruto.
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.
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.
Well, it could be Orochimaru. He was always up to no good and had an interest in powerful ninja. He might target Naruto and Temari to either steal their powers or use them for his evil experiments, which would surely lead to them getting hurt.
Perhaps some rogue ninja from other villages. They might see Naruto as a symbol of Konoha's power and want to take him down to weaken Konoha. These rogue ninjas could be led by a powerful and vengeful shinobi who has a grudge against Konoha. So when Naruto is alone on a mission or something, they attack, and that's when Minato steps in to save him.