Bane could also be the main villain. He's strong enough to physically challenge Batman and has a complex backstory. He could be planning to break Batman both physically and mentally in the game story.
Ra's al Ghul is another option. He has different motives compared to other villains. He wants to 'cleanse' the world in his own way, which often puts him at odds with Batman. His long - lived existence and access to powerful resources would make for a great main villain in a Batman game story.
Lex Luthor would be a great choice. He could be plotting against both Batman and Supergirl. He might try to use his intellect to create a weapon that can nullify Supergirl's powers and outwit Batman's strategies at the same time.
Another option could be a new villain created specifically for the fanfic. This villain could be someone who has a vendetta against the Wayne family because of something Batman's dad did in the past. He could be a master of disguise and manipulation, making it difficult for Batman and his dad to figure out who he really is.
The Joker could be a main villain. He might see Izuku as a new plaything and try to break his spirit during his training with Batman.
Perhaps an old enemy of Batman who has made a deal with Cadmus. They combine their knowledge and resources. This could be someone like Mr. Freeze, who has found a way to use Cadmus' genetic engineering to make himself even more powerful. His new form and abilities would pose a great challenge for Batman Beyond.
Ink could be a great main villain. He's a character from the Batman Beyond series known for his ability to manipulate ink - like substances. He could target Robin specifically, seeing him as a weak link in the Batman - Robin duo. His powers would pose a unique challenge for Robin to overcome.
Ra's al Ghul could also be a main villain. He might see the child of Batman and Catwoman as a potential weapon or a threat to his plans for Gotham. He could try to either recruit the child to his side or eliminate them, which would put Batman and Catwoman in a difficult position as they fight to protect their family from Ra's al Ghul's devious schemes.
Lex Luthor would be a great choice. He's Superman's long - time nemesis. He could form an alliance with some of Batman's foes like the Joker. Luthor could use his intelligence and resources to create a plan that only Superman and Batman together could stop.
The Reverse - Flash could be a great main villain. He could travel to Gotham to cause chaos and draw out the Flash. His time - manipulation abilities would pose a huge threat not only to the Flash but also to Batman's carefully planned strategies in Gotham. Batman would have to adapt to dealing with a villain who can move at super - speed and mess with time.
The Joker could be a great villain. Imagine if the Joker - like character emerged in the My Hero Academia world. Izuku, with his new Batman - inspired skills, would have to use his wits to outsmart this chaotic and unpredictable foe.
Kingpin would be a very suitable main villain. He has his criminal empire in Hell's Kitchen already, and if he decides to make a move on Gotham, it would bring him into conflict with Batman. His power, wealth, and ruthlessness would make him a formidable foe for the two heroes to face together.