A group of rogue ninja from the other dimension could also serve as the main antagonists. They might be jealous of Naruto's power from his original dimension and want to steal it for themselves. They could be led by a charismatic and devious leader who has a personal vendetta against Naruto for some reason, like he believes Naruto will disrupt their way of life in the dimension.
A powerful dark wizard could be the main antagonist. This wizard has been ruling the other dimension with an iron fist and sees Peter as a threat to his power. He uses his dark magic to create all kinds of obstacles for Peter, from summoning monsters to casting spells that distort Peter's perception of reality.
It could be an alternate version of Orochimaru. Maybe in this new dimension, he has achieved ultimate power and is using it to control the different ninja villages.
Perhaps a group of rogue time - traveling wizards. They come from a future in this dimension where the wizarding world has been destroyed, and they believe that changing the past (even if it means causing chaos) is the only way to save their future. They see Harry as a threat to their plans because he has a natural inclination to preserve the present order.
Maybe it's a corrupted version of one of the gods from Percy's world who has gained even more power in this new dimension. They could be trying to spread chaos and destruction, and Percy has to stop them. This antagonist would know Percy's weaknesses from their time in the original world, which would make the conflict more intense.
It could be a corrupted version of one of the Fairy Tail members from the other dimension. For example, an evil Natsu who uses his fire magic for destruction and domination. The real Natsu would have to face his own dark self and find a way to defeat him without losing his own identity.
Perhaps a group of elite warriors in the new world who are jealous of Naruto's unique abilities. They form an alliance to take him down because they fear he will disrupt their status quo and take over their positions of power.
A powerful and corrupted duelist from a forgotten dimension could be the main antagonist. This duelist might have discovered a way to harness the power of the dimensional rifts for his own evil purposes. He could be using this power to create chaos and destruction across all the dimensions, and only the combined efforts of the heroes from different dimensions can stop him.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Naruto could meet alternate versions of his friends or enemies. For example, he might find a version of Sasuke who has a completely different personality or a different set of skills. This would create interesting interactions and potential conflicts or alliances.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.