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.
Another likely villain could be Mr. Sinister. He has a long - standing interest in mutants. In a crossover, he might expand his operations to Gotham, either looking for new test subjects or trying to find a way to use Batman's resources. His scientific knowledge and ability to manipulate mutants would put him at odds with Wolverine, and his criminal activities would draw Batman's attention.
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.
The Riddler could be very interesting. He could create complex riddles that not only test Batman's detective skills but also stump Spiderman. His maniacal love for puzzles could be a great contrast to the more straightforward villains that Spiderman usually faces.
The Joker would be really interesting. Imagine him getting his hands on some of Oscorp's dangerous technology. He could use it to create chaos in both Gotham and New York in ways that neither Batman nor Spiderman have seen before. His unpredictable nature would make it hard for the two heroes to anticipate his moves.
Another possible villain could be Fenrir Greyback. He is a werewolf in the Harry Potter world, and Wolverine also has some werewolf - like qualities. Fenrir might see Wolverine as a rival. He could team up with some dark wizards to try and take down Wolverine and Harry Potter. This would create a complex web of battles and power struggles between different factions in the fanfiction.
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.
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.
Definitely the Bat - family. Robin, Nightwing, Batgirl, etc. would be there to pay their respects. Alfred, who has been like a father figure to Batman, would also be present. And of course, Commissioner Gordon, as he has been Batman's ally in the fight against crime in Gotham for a long time.
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.