Lex Luthor could also be a possible main antagonist in this crossover. If he somehow gets transported to the RWBY world, he might see the chaos and the power sources like Dust as opportunities. He could form an alliance with some of the RWBY villains, using his intellect to create weapons and strategies to take on Superman while also causing trouble for the RWBY teams.
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.
Maybe an ancient being that was sealed away long ago in the RWBY world but has now been awakened by Naruto's arrival. This being, with its own set of dark powers, sees Naruto as a threat to its plans of domination. It starts to create chaos, summoning Grimm in large numbers and using some form of corrupted chakra - like energy to attack. The RWBY characters and Naruto would have to put aside their differences and combine their skills to defeat this powerful foe.
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 new character created specifically for the fanfiction could be the main antagonist. For example, a powerful being from another dimension who is attracted to the chaos in Remnant caused by the combination of RWBY and Starkiller's presence. This character could have abilities that are a threat to both Starkiller and the RWBY characters, forcing them to work together in ways they haven't before.
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.
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.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
There could be an ancient evil entity that was sealed away long ago in Vacuo. Due to some recent events, it starts to break free. It corrupts the minds of some of the King's men and tries to use them to get rid of the King and RWBY, who are the only ones who can stop it from fully emerging and causing destruction.
It could be a power - hungry general from one of the warring factions. Someone who is willing to sacrifice anything and anyone to achieve victory.
The God of Creation himself could turn out to be the main antagonist. He might start off as a benevolent figure but then reveal his true, more self - serving motives. Maybe he wants to reshape Remnant in his own image, regardless of the cost to its inhabitants.