Another option could be a dark magical entity that feeds on negative magic. Since the worst witch is trying to change and become more positive, this entity feels its power source is being threatened. So, it becomes the main antagonist, trying to draw her back into her old, chaotic ways of using magic.
Maybe a powerful and strict magic council member who has a grudge against the idea of second chances. He or she sees the worst witch's new start as a threat to the order and rules of the magic world and tries to stop her progress at any cost.
A great plot might involve the worst witch losing all her magical abilities due to a powerful curse. However, instead of being discouraged, she decides to start from scratch and learn non - traditional forms of magic. Along the way, she uncovers secrets about the origin of magic itself and uses this knowledge to not only regain her powers but also to become a more respected and powerful witch in a completely new way.
Perhaps a powerful business tycoon who is trying to take over the land where she lives. He sees her as a threat because she is trying to protect the natural resources and the people there. He uses his money and influence to create all sorts of obstacles for her.
A new Titan could emerge as the main antagonist. Maybe one that was hidden away all this time and now has awakened to seek revenge on the demigods. This Titan could have unique powers that the demigods have never faced before.
Perhaps an old, powerful shinobi who was thought to be dead but has now returned in Naruto's new life. This shinobi could be seeking to reshape the ninja world according to his own dark vision, and Naruto would have to stop him. The antagonist might have some connection to Naruto's past life that is gradually revealed as the story progresses.
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.
It could be an old rival who has also gained some sort of dark god - like powers. For example, Sasuke could have been corrupted by a powerful dark force while seeking more power, and now he stands in Naruto's way as he tries to use his new god - like abilities for good.
Perhaps an old enemy from Naruto's past, who has somehow been resurrected with a new power and a new purpose. This enemy could be someone like Orochimaru, but with even more sinister motives and abilities. He might want to take over the world in a different way than before.
An old enemy of the Omnitrix's creator could be a great main antagonist. Maybe this enemy was locked away for centuries and now has escaped and blames the Omnitrix for his imprisonment. He would be extremely powerful and have knowledge of the Omnitrix's weaknesses that Ben doesn't even know yet.
Maybe the main antagonist is a dark entity from another dimension. It has no real form, but it can possess people and make them do its bidding. It targets Annelixa because she has the power to stop it from spreading its chaos to her world. So it sends all kinds of minions and creates difficult situations for her to deal with.
It could be a rogue ninja who is jealous of Naruto's new look. This ninja might see Naruto's new appearance as a sign of great power and wants to take it for himself. So, he would constantly try to attack Naruto and steal his power, which would lead to a series of battles between them.