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.
Well, it could be about Annelixa facing a great challenge in a new world. Maybe she has to fight against a powerful dark force that threatens her homeland. This would involve a lot of action scenes, like epic battles with magic and swords.
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.
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.
It could be a rogue ninja who was once a part of Konoha but was banished for unethical experiments. Now, with a thirst for revenge against Naruto and the village, he returns as a powerful and unpredictable foe.
It could be a rogue scientist who was once part of the team that created Stitch. This scientist could be jealous of Jumba's success and wants to use Stitch for his own evil purposes.
Madara Uchiha might be the main antagonist. He has grand plans for the ninja world. He could see Naruto as a threat to his vision and engineer a situation in the Valley of the End where Naruto is killed, either directly or by using Sasuke as a pawn.