Darkseid could also be a great antagonist. Imagine the protagonist, as the newly reborn Superman, having to face the might of Darkseid so early in his new life. Darkseid's goal of universal domination would put him directly in conflict with Superman, who stands for truth and justice.
Lex Luthor would be a classic choice. He could be jealous of the protagonist who is reborn as Superman and see him as a threat to his own power and influence. Luthor might try to use his intellect to create new weapons or strategies to defeat Superman.
A possible main antagonist could be a powerful alien who sees Naruto as an abomination. This alien might come from Krypton and believe that Naruto, as a clone of Superman, is a perversion of their species' power. The alien would have all the typical Kryptonian powers but with a more malevolent intent. He would try to destroy Naruto and the Hidden Leaf Village, thinking that he is doing a service to the universe by eliminating this 'false' Superman.
Maybe Salem could be the main antagonist. She has been a long - standing evil force in the RWBY world. If Superman shows up, she would likely view him as an obstacle to her ultimate goal of destroying the world and remaking it in her image. She could use her Grimm army and her own dark magic to fight against Superman and the RWBY characters.
Lex Luthor could be a great antagonist. He might see Rogue Lemon as a new variable in his plans to defeat Superman. He could try to manipulate Rogue Lemon into turning against Superman or use her powers for his own evil purposes.
It could be a combination of Orochimaru and Lex Luthor. Orochimaru from the Naruto universe is always seeking power and Lex Luthor from the DC universe is a brilliant but evil mastermind. They could team up, with Orochimaru being interested in Superman - like Naruto's unique physiology and Lex Luthor wanting to use Naruto's power to take over both the Naruto world and the DC world. They would be a formidable duo, constantly devising plans to undermine Naruto and his friends.
Maybe an alien race that doesn't approve of Superman marrying a human. They could send an agent to Earth to try and stop the marriage. This agent could have powers similar to Superman's and create a lot of trouble for the couple, both in their personal lives and in their superhero duties.
A powerful and ancient Kryptonian entity that was sealed away long ago could be the main antagonist. It breaks free due to some events and wants to reshape Krypton according to its own dark desires. The reborn character, with their new - found powers and different perspective, stands in its way. Also, there could be a group of Kryptonian zealots who oppose any change in the traditional Kryptonian ways. They see the reborn character as a threat to their way of life and try to get rid of them.
It could be a new character created specifically for the fanfiction. Maybe a powerful pirate who has a vendetta against the Straw Hat crew because of the oc's presence. Since the oc is reborn into this world, they might bring some sort of change that angers this new antagonist.
It could be a new character who has the ability to disrupt both Lambo's time - traveling powers and the Reborn characters' mafia - based powers. This antagonist might be after a powerful artifact that Lambo and the Reborn crew are protecting.
The goddess Hera might also be a great antagonist. Since she has a history of interfering in the lives of demigods, she could be jealous or threatened by Percy's rebirth. She might try to stop him from reaching his full potential in his new life or cause trouble between him and his new allies.
The Green Goblin could be a great main antagonist even in a Spider Man reborn story. Maybe in this version, he has developed a new form of insanity - inducing gas that affects Spider Man's new powers. Another possibility is Doctor Octopus. He could have found a way to merge his mechanical arms with some sort of alien technology, making him far more powerful and a real threat to Spider Man reborn.