Ra's al Ghul could also serve as the main antagonist. He might have a new plan for Gotham that involves using Catwoman as a pawn. He could be aware of her relationship with Batman and try to use it to his advantage. Batman would have to not only save Gotham but also rescue Catwoman from Ra's al Ghul's clutches.
The Penguin could be a great antagonist. He might mock Catwoman for her weight gain, using it to try and undermine her confidence and take over her territory in Gotham.
The Queen of Hearts could be the main antagonist. She is known for her tyrannical rule in Wonderland. Her desire for absolute control could put her at odds with Batman, who is used to fighting against those who abuse power in Gotham. She might see Batman as a threat to her reign and try to eliminate him.
Ra's al Ghul would also be a great choice. His knowledge of the occult and his desire to cleanse the world in his own way could put him at odds with the power of the Witchblade. He might see it as a tool that could either be used for his own ends or something that needs to be destroyed to maintain his version of order in the world. Batman would be caught in the middle, trying to protect Gotham and the wielder of the Witchblade from Ra's al Ghul.
The Joker could be a great antagonist. His chaotic and unpredictable nature would contrast with Naruto's more straightforward sense of justice.
Maybe there's an Amazon who has turned against her sisters and sees Batman's arrival as an opportunity to gain power. She could try to use Batman's technology for her own evil plans, and Batman would be caught in the middle between her and the rest of the Amazons.
It could be a jealous artist named Max. Max has always been overshadowed by Bendy and Betsy's talent. So, he devises a plan to steal their ideas and take over the art world in their story. He starts spreading rumors about Bendy and Betsy to turn other artists against them.
It could be an evil shinobi who wants to disrupt the meeting between Naruto and Kushina. Maybe they know that Kushina has some special knowledge or power that she could pass on to Naruto, and they don't want that to happen.
It could be a rogue Sound ninja who has his own agenda. Maybe he wants to start a war between Konoha and the Sound Village to gain power in the chaos. He would see Naruto as a threat to his plans and try to eliminate him.
A powerful and corrupt World Noble could be the main antagonist. They might be trying to stop both Luffy and Dragon's efforts for freedom. The World Noble could have a large military force under their control and be causing chaos and oppression in various parts of the world. This would force Luffy and Dragon to join forces to take them down.
The Riddler could be a great main antagonist. He could use his knowledge of time paradoxes and puzzles to try and outwit Batman as he travels through time. He might set up elaborate traps across different time periods that Batman has to solve.