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.
The theme of friendship also pops up a lot. As Tenten travels through time, she forms new friendships or strengthens existing ones. For example, she could bond more with Naruto or Sakura in a different time period. Also, the idea of fate versus free will is a common theme. Tenten might think she can change things but then realizes that some events are meant to happen no matter what she does. It makes for an interesting exploration of the Naruto universe's concepts.
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.
Maybe some new rogue ninja group that has a vendetta against the Uzumaki family. They see Boruto as a way to strike at Naruto, so they try to harm him, which then leads to Naruto having to save him.
There could be internal antagonists within Naruto's own village. Some of the more conservative ninja in the village might not trust Naruto's new - found skills and powers obtained from Zetsu. They could try to undermine Naruto or even attempt to exile him, fearing that he has been corrupted by Zetsu's teachings.
The Akatsuki could still be the main antagonists. Since Naruto is being trained by Shisui, they would see Naruto as an even greater threat. His new skills under Shisui's training could put their plans at risk. For example, if Naruto becomes better at stealth and infiltration, he could disrupt their operations more effectively.
It could be some rogue ninja clans that are after Karin for her special abilities. They might see her as a tool to gain power or information. For instance, a clan that specializes in blood - related jutsu might want to use Karin's unique blood - sensing ability for their own evil purposes.
The village elders could be antagonists. They might see Naruto and Kakashi as threats to their traditional way of ruling the village and use false accusations to banish them.