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.
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.
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.
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.
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 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.
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.
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.
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.