Who could be the main antagonist in a 'naruto time travel academy fanfic'?
Danzo could also be a main antagonist. He has always had his own agenda in the Naruto universe. In the academy setting, he might try to use Naruto's time - traveling situation for his own benefit, or he could be trying to cover up some secrets that Naruto is about to uncover. He is a shadowy figure who could create a lot of conflict for Naruto during his time at the academy.
It could be Orochimaru. Even in the academy days, he was already plotting and scheming. If Naruto time - travels back, Orochimaru might see him as a threat to his early plans and target him. Orochimaru's thirst for power and knowledge makes him a great antagonist for this scenario.
Another option is a time - traveling version of one of the Akatsuki members. For instance, if a member like Itachi time - travels to the academy days for some reason related to Naruto's future actions, he could become an antagonist. He has the power and the mystery around him to pose a significant threat to Naruto and the other academy students.