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.
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.
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.
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.
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.
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.
Perhaps another reborn character could be the main antagonist. Say, an evil sorcerer from the past who was also reborn in the Inuyasha world at the same time as the OC. This sorcerer has his own agenda of ruling the world and sees the OC as a threat to his plans, especially if the OC is getting in the way of his attempts to gather the Shikon Jewel fragments.
It could be an ancient evil that was sealed away long ago but has been released due to Naruto's death. Maybe Naruto's sacrifice in his previous life weakened the seal, and now this evil has emerged. It could be a powerful demon or a dark ninja with extremely strong and malevolent jutsu.
It could be a group of Team Rocket - like villains. They are after the unique powers that the reborn pokemon might possess. Since the reborn pokemon has a human - like intelligence, they see it as a valuable asset to use for their evil plans, like stealing all the precious pokemon resources or taking over a certain region.