It could also be Bane. His brute strength and strategic mind would pose a serious threat. Bane might see Naruto as a threat to his plans of taking over Gotham. And Naruto would have to use his agility and ninja techniques to counter Bane's physical power, while Batman uses his intellect and gadgets to outwit him.
Maybe Ra's al Ghul. He has his own ideas about justice and order which would clash with both Naruto and Batman. He could see Naruto as an interesting new element in his plans for Gotham or the world at large. His immortality and combat skills would make him a formidable foe for Naruto and Batman to face together.
The Joker could be a great antagonist. His chaotic and unpredictable nature would contrast with Naruto's more straightforward sense of justice.
The Joker could also be a main antagonist in this fanfic. He could be interested in causing chaos not only in Gotham but also in the world of Wonder Woman. His unpredictable nature and love for mayhem would make him a formidable foe for the two heroes. He might come up with a plan that plays on their differences and tries to drive a wedge between them while also causing destruction.
A powerful rogue ninja who has mastered a forbidden jutsu that gives him the ability to control minds could be a great main antagonist. He could use this power to turn Naruto's friends against him, creating a lot of internal conflict within the group.
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.
It could be Ra's al Ghul. He's always interested in things that can give him an edge in his quest for immortality. If he discovers the power of chakra in the Naruto world, he might try to take over both worlds. His skills as a master assassin and his vast resources would pose a huge threat to Naruto and Batman, who would have to put aside their differences to defeat him.
It could be an older and more powerful version of Orochimaru. In the new game plus scenario, he might have found a way to cheat death completely and has amassed an even greater army of experimental ninjas. He could be the main antagonist as he tries to take over the ninja world with his new - found powers and knowledge.
It could be a new villain created specifically for this fanfiction. Maybe a powerful ninja - like figure from another dimension who is jealous of Naruto's powers and wants to take them for himself while Naruto is in the Batman universe and feeling neglected, so he has to fight this new threat alone at first.
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.
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.
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.