The Batman Who Laughs could also serve as the main antagonist. He represents a twisted version of Batman, and his goal could be to infect all the Batverses with his madness. His knowledge of Batman's tactics and his own insanity would pose a huge challenge for the normal Batman as he tries to stop him from spreading chaos.
The Joker could be a likely main antagonist. He might be the one who manipulates the situation to get Batman arrested, perhaps by framing him for one of his own heinous crimes. The Joker loves to play mind games, and getting Batman locked up would be a huge part of that.
The Joker is always a great choice. He could come up with a particularly cruel and elaborate plan to put Batman in peril, like kidnapping all of Batman's allies and forcing him to choose which ones to save.
The Joker could be the main antagonist. Even though Batman is in jail, the Joker could find a way to continue his chaos - making. He might try to get into the prison to torment Batman or use the situation to his advantage by causing mayhem in Gotham City without Batman there to stop him.
Darkseid could be a potential main antagonist. He might view Superboy as a weapon that he wants to control. If he realizes that Batman is trying to shape Superboy into a hero of Earth, he would surely try to stop it. He could send his minions to attack Batman and Superboy or try to corrupt Superboy's mind from afar with his Omega Beams.
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.
The Joker could still be the main antagonist. He might find the idea of Batman being a girl extremely hilarious and try to use it to his advantage. Maybe he would try to play mind games with her, thinking that she would be more vulnerable in her new form.
The main antagonist could be a deranged chemist who was once shunned by the scientific community. He uses his knowledge of chemistry to create deadly toxins and gases to get revenge on those who wronged him. He sees Batman and Robin as obstacles in his path of destruction.
Ink could be a great antagonist. He has the ability to manipulate his body into various weapons and forms. He could be seeking to take over Gotham's underworld in the 'Batman Beyond' era and sees Nightwing and Batman Beyond as threats to his plans.
The Joker would be a great antagonist. He could be the one who creates the situation where Batman is in a diaper, perhaps as part of some elaborate and twisted prank. He'd find it hilarious to see the Dark Knight in such a vulnerable state and would use it to his advantage to cause chaos 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.