Another possibility is that Orochimaru could be a main antagonist. He has always been interested in power and experimenting on people. He might see Naruto's control over Sakura as something he wants to either steal or disrupt for his own evil purposes.
It could be the Akatsuki members. Since they are often the main villains in the Naruto universe, they might also play that role in this fanfiction. They could be trying to stop Naruto from using his control over Sakura to achieve something that would be a threat to their plans.
It could be some of the traditional power - hungry ninja clans who oppose Naruto's new world order. They might see his attempts at global control as a threat to their own interests and try to undermine him.
The Akatsuki members might also be antagonists. Since they're after the tailed beasts, Naruto with his additional power of lightning control would be a prime target. They might send their most powerful members like Pain or Itachi to deal with him.
It could be the Akatsuki. Since Naruto has this new power of controlling space, they might see him as an even greater threat and target him more aggressively. Their own powers and goals would likely clash with Naruto's new - found abilities.
Often, it could be a group of rival students from another college who are jealous of Naruto and Sakura's skills or achievements. They might try to sabotage their projects or disrupt their college events.
Often, Orochimaru can still be a main antagonist in these fanfictions. He might have some new, devious plan related to the Chunin Exams, like using the chaos of the exams to steal some powerful jutsu or secrets from the village.
In a few fanfictions, it could be a jealous ninja within the village. Maybe someone who has feelings for Naruto and sees Sakura as an obstacle. This ninja could create a false narrative that leads to Sakura's banishment, thus becoming the main antagonist in the story.
It could be an original character created just for the fanfiction. Maybe a powerful ninja from a forgotten clan who has a vendetta against Konoha and targets Naruto, Sasuke and Sakura specifically.
There could be a group of mean students who don't like Naruto because he's different. They constantly bully him and try to keep him away from Sakura. They might be the typical 'popular' kids who think Naruto doesn't belong in their school or around Sakura.
Well, obviously Sakura is one of the main characters. She is the one with the power to control dragons. And then there are the dragons themselves, which can be individual characters with different personalities. For example, there might be a wise old dragon that acts as a mentor to Sakura.
In some fanfictions, there could be a group of rogue ninjas who form an alliance during the war. They have no loyalty to any particular side and are only interested in causing mayhem. Sasuke and Sakura would have to deal with their unpredictable attacks and devious plans.