Orochimaru might also be an antagonist. If they travel to a time when Orochimaru was still active in Konoha, he could be interested in Sasuke's power and Hinata's unique abilities. He might try to use them for his own experiments or gain some knowledge from them against their will.
The Time - Travel itself could be an antagonist in a sense. There could be some rules or forces in the time - travel mechanism that don't want them to change the past. So, Sasuke and Hinata have to constantly fight against these unseen forces while also dealing with the normal threats in the past.
Danzo could be a potential antagonist. Even in the past, he might be plotting against the Uchiha clan. If Sasuke and Hinata try to change things related to the Uchiha, Danzo could see them as a threat and try to stop them.
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.
Some of the remaining members of the Akatsuki who still hold grudges against Sasuke or see the baby as a threat to their plans. They might target the baby to get revenge on Sasuke or to use it as a bargaining chip. For example, if there are any Akatsuki members who were loyal to Itachi and don't like Sasuke's new life with Naruko, they could cause trouble for the family.
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.
One common theme is redemption. For example, Hinata might travel back in time to try and save Sasuke from his darker path. Another theme is the exploration of alternate relationships. Since Hinata and Sasuke don't have a major relationship in the original Naruto series, in these fanfictions, their relationship gets explored in new and interesting ways.
Their relationship would likely become closer. Sharing the experience of time travel would create a unique bond. Sasuke might start to see Hinata in a new light, noticing her courage and determination. Hinata would also get to know Sasuke on a deeper level, understanding his past traumas better.
One idea could be that Sasuke and Hinata travel back to the time when the Uchiha clan was still intact. Sasuke gets to see his family again and Hinata witnesses the power and unity of the Uchiha. They might try to prevent the tragedy that befell the Uchiha clan. Another plot could be them traveling to a future version of their world that has been completely destroyed. They then have to figure out how to go back in time to change the events that led to this destruction.
One common theme is redemption. For example, Sasuke might go back in time and try to fix the wrongs he did in the original timeline. Another theme is love. Hinata might use the time travel to get closer to Naruto earlier or in a different way.
One popular Sasuke Hinata time travel fanfiction is 'A New Path'. In this story, Hinata travels back in time and tries to change certain events related to Sasuke. It has an interesting plot where Hinata's knowledge of the future gives her an edge in dealing with the complex relationships in the Naruto universe.
One potential antagonist could be a rogue ninja from another dimension who wants to use Naruto and Naruko's abilities for his own gain. He might be jealous of their power and try to trap them in different dimensions to study their techniques. Another could be a powerful entity that controls the portals between dimensions and doesn't want Naruto and Naruko messing around with the balance of different worlds.
A jealous courtier could be an antagonist. Maybe someone in the princess's own court who is envious of her position and tries to stop her time - travel adventures out of spite or to gain power for themselves.