Maybe a mysterious figure from outside the academy's timeline. This person is jealous of the power the academy holds and wants to use Ichigo's time - traveling ability to get inside and destroy it from within, believing that the academy's existence disrupts the balance of the universe.
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.
There could be a group of corrupted Quincy who view Ichigo's resurrection as an abomination. They believe that his power goes against the natural order of things. So, they band together to try and eliminate him. They might have some new and dangerous weapons or techniques specifically designed to counter Ichigo's resurrected powers. This group could be led by a very powerful Quincy who has a personal vendetta against Ichigo or the Soul Reapers in general.
Perhaps a new character created specifically for this fanfiction. This new antagonist could be someone who wants to use the power of reincarnation and time travel for their own evil purposes, like trying to rewrite the world to their liking and is opposed by Ichigo and Kaien.
Aizen could still be the main antagonist. Even if Ichigo travels back in time, Aizen's long - term plans might be already in motion. Ichigo would have to find a way to expose and stop Aizen earlier than in the original timeline.
Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
It could be a time - traveling sorcerer who wants to change history for his own evil purposes and sees Achilles as a threat. The sorcerer might try to stop Achilles from getting back to his own time or use his knowledge of the future to his advantage against Achilles.
A time - traveling bounty hunter could be the main antagonist. He might be after Lucy because she has somehow disrupted the time - space continuum. He's cold - hearted and will stop at nothing to bring her to some time - traveling justice.
Perhaps an ancient evil that was sealed away long ago but is released due to Temari's time - traveling disruptions. This evil entity then starts causing chaos in the past, and Temari is the only one who can stop it with her modern skills and knowledge.
It could be a time - traveling villain from the future who wants to change the past to gain more power in their own time. They might try to stop Naruino from achieving their time - travel goals.