Darkseid is another option. His power and his desire to conquer Earth could bring Batman and Superman together. He could target both Metropolis and Gotham, and his presence would require the two heroes to combine their skills. Batman's strategic mind and Superman's brute strength would be needed to face this powerful foe.
Lex Luthor. He's always looking for a way to take down Superman, and an apocalypse would be the perfect time for him to make his move. He could be using the chaos to build some sort of doomsday device or manipulate events to his advantage.
Brainiac could also work well. He is an android with an insatiable thirst for knowledge and a penchant for collecting and destroying planets. In a crossover, he could target Earth, specifically Gotham and Metropolis. His advanced technology would pose a major challenge to both Superman and Batman. Superman's super - powers would be put to the test against Brainiac's powerful defenses, and Batman would need to use his wits to find a weakness in Brainiac's systems, leading to an exciting and complex story.
Ra's al Ghul could be a great villain. He is always seeking power and immortality. In a crossover, he might see the potential in mutant genes to achieve his goals. His vast resources and knowledge would make him a formidable foe for both Wolverine and Batman. He could be plotting to use mutants in some grand scheme that would also impact Gotham, which would draw the attention of both heroes.
Harley Quinn is an obvious choice. Her obsessive love for the Joker could be transferred to Batman in a fanfiction harem scenario. She's unpredictable and could add a lot of chaos and humor to the group. Then there's Poison Ivy. Her connection to nature and her alluring charm would make her a likely candidate. She could use her plants to protect the harem or create a private sanctuary for them.
Alfred is always a likely ally. His knowledge and experience can provide valuable support to Batman. Also, Oracle (Barbara Gordon) could be an important ally, using her hacking skills to disrupt any technology Superman might use or to gather information.
Wonder Woman could also be involved. She might be caught in the middle, trying to stop the fight at first. But if she realizes that Superman is being a threat for some reason, she could side with Batman, or at least not interfere in Batman's attempt to defeat Superman.
The Reverse - Flash would be really interesting. He could target both Batman and the Flash. For the Flash, he's a long - time nemesis, but for Batman, he'd be a new and extremely dangerous threat. His ability to manipulate the speed force and time could put Gotham in chaos in ways Batman has never seen before. And he could use his knowledge of the Flash to try and set traps for both heroes.
Kabuto could be a likely villain. He's very intelligent and has a thirst for power. He could use his knowledge of jutsu and his ability to manipulate others to try and steal The Flash's speed force. He might think that by combining it with his own powers and ninja techniques, he could become invincible.
Lex Luthor could be a great villain. He might be jealous of Supergirl's powers and see Flash as an obstacle in his plan to defeat her. He could use his scientific knowledge to create some sort of weapon that targets both speedsters and Kryptonians.
The Joker could be a great villain. Imagine him getting his hands on some ghostly technology or artifacts from Danny's world. He would use it in his own chaotic and unpredictable way, causing mayhem in Gotham and also attracting Danny's attention. Danny and Batman would have to work together to stop the Joker's mad schemes.