A powerful sorcerer who wants to harness the power of the earth and sky for his own selfish gains could be a great antagonist. He might try to corrupt the natural balance to gain unlimited power.
It could be a dark entity that was once a part of the earth and sky but became corrupted. This entity now wants to spread chaos and destruction, seeing the harmony between the earth and sky as something to be broken. It uses its knowledge of the earth and sky's secrets against the protagonist.
Maybe an industrialist who doesn't care about the balance of the earth and sky. He wants to exploit the resources of the earth and disrupt the sky's natural order for his business. He sees the main character, who is trying to protect the earth - sky connection, as an obstacle to his plans.
It could be a corrupt politician. This person uses their power and influence to control the city or country Naruto lands in. They see Naruto as a threat to their power and try to get rid of him. They might hire assassins or use their own military - like forces against Naruto.
Another possibility is that Naruto himself could be his own antagonist in a sense. His loneliness and the weight of being the last man on earth could drive him to the brink of madness. He might have to fight his own inner demons, which could be manifested as a dark version of himself that wants to give up on the world and just let it decay.
It could be a powerful demigod who has been corrupted by greed. He wants to use the power of the earth for his own gain, like creating his own kingdom or something. So he's trying to stop Percy from protecting the earth because Percy stands in his way.
A group of rogue sky spirits might serve as the main antagonists. They are jealous of Percy's status as the 'Son of the Sky' and want to steal his powers. They could be constantly causing chaos in the sky, like creating dangerous storms and attacking flying creatures. Percy would have to figure out their motives and stop them before they cause too much damage. These sky spirits could have their own hierarchy and leader, making them a formidable foe.
It could be Doctor Octopus. Imagine he somehow gets his hands on some Sky High technology that enhances his mechanical arms and gives him new powers. He then decides to take on both Spider - Man and the Sky High students because he sees them as threats to his new - found power and his plans for world domination.
It could be a jealous wizard who was once in love with Hermione. Discovering she has a child with Fred, this wizard might seek to harm the child out of spite. He could use dark magic to try and kidnap the child or cause trouble for the family.
Perhaps an old enemy of Naruto or Sakura who was thought to be defeated but actually survived. They see the child as an easy target to get back at their parents. For example, if there was a rogue ninja from their past who held a grudge, they could come back and try to use the child to draw Naruto and Sakura into a trap. This antagonist would be very cunning and know all the weaknesses of Naruto and Sakura, which they could try to exploit through the child.
It could be a distant relative of Voldemort who has been biding their time in the shadows. They might have a vendetta against the Potter family for what happened to Voldemort. This relative could be secretly gathering followers and planning to strike at the second child when they least expect it.
It could be a descendant of one of the Death Eaters who holds a grudge against the Potter family. They might try to finish what Voldemort started and target Albus specifically.
The main antagonist could actually be Anakin's own self - doubt. Since he's in a child's body but has an adult's memories, he might struggle with feelings of inadequacy. This internal struggle could act as an antagonist, preventing him from fully embracing his new situation and using his abilities to the fullest. It could be a psychological battle within himself that holds him back more than any external foe.