Catwoman would also be a great addition. She has a long - standing, complex relationship with Batman. In a harem, she could be the one who tries to maintain some level of normalcy and order, while also having her own motives for being there. Another possible member could be Talia al Ghul. Her ties to the League of Shadows and her own feelings for Batman would make her a powerful and interesting part of the harem. She might bring in elements of mystery and international intrigue.
The Penguin could be an unexpected but interesting member. His wealth and influence in Gotham's underworld could be used to support the harem in terms of resources. And despite his rather odd appearance, in a fanfiction world, there could be some strange attraction or bond with Batman. Also, Two - Face, with his dual personality, could add a lot of drama and conflict within the harem, constantly wavering between loyalty and betrayal.
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.
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.
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.
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.
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.
It could be an evil Sith Lord who discovers the existence of the Naruto universe and wants to conquer it. He sees Naruto and Ahsoka's alliance as a threat and tries to stop them. This Sith Lord might use his dark side powers to corrupt some of the characters from the Naruto universe and turn them against Naruto and Ahsoka.
Voldemort would still be a very likely villain. He would see the Hulk as a threat or a tool to be used for his own evil purposes. He might try to control the Hulk's mind or use dark magic to make the Hulk do his bidding.
It could be Orochimaru. His thirst for power and his willingness to experiment on others would put him at odds with both Naruto and Deadpool. Orochimaru might see Deadpool's regenerative abilities as something to study and Naruto as a threat to his plans. He could try to capture them and use their powers for his own dark purposes.
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 Green Goblin could be a likely villain. He has a long history with Spiderman and his maniacal nature would put him at odds with both Spiderman and Deadpool. His glider and pumpkin bombs would be a real threat to them.