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.
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.
Danzo could also be a common antagonist. He was very power - hungry and had his own dark secrets. In a time - travel scenario, he might view Kakashi and Naruto as threats to his control over the Hidden Leaf Village in the past. He could try to eliminate them to maintain his grip on power.
Often, the main antagonists can be the village elders or some corrupt shinobi within the village who are behind their banishment. These characters may fear Naruto and Naruko's growing power and influence.
Another theme is power - up. Since they have knowledge from the future, they can train more effectively or use future - knowledge - based strategies to become stronger. For instance, Naruto could use his knowledge of future battles to develop new jutsus faster. It's also about changing destiny. They don't want to accept the future as it was in their original timeline and strive to create a better one for themselves and their village.
One common theme is redemption. They often go back in time to correct past mistakes, whether it was Naruto's lonely childhood or some major events that went wrong in the original storyline. For example, in many fanfictions, they try to save characters who died in the original plot.
It could be Orochimaru. Even though he was defeated before, he might come back with a new plan. Maybe he wants to use Naruto and Naruko's family for some dark experiment, like trying to extract the unique chakra combination that their family might have.
Maybe a new organization of rogue ninjas that see Naruto's Rinnegan as a threat to their own goals of taking over the ninja world. They target Naruko as a way to get to Naruto. These ninjas could have some unique and powerful jutsus of their own, making them formidable antagonists.
It could be some powerful dimension - hopping villains who want to use the power of different dimensions for their own evil purposes. They might see Naruto and Naruko as threats to their plans.
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.