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.
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.
The main baddie in 'Batman Hush' from DC graphic novels is Hush. This character is not just any ordinary villain. He has a personal vendetta against Batman. His identity is part of the mystery that drives the story forward. He is smart, calculating, and his actions are designed to not only defeat Batman physically but also psychologically.
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.
It could be someone like Ra's al Ghul. He is a powerful and complex villain that both Batman and The Shadow would have a hard time dealing with. His global influence and long - life plans would pose a great threat to their efforts to protect Gotham and the world.
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.