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 Joker is probably one of the most popular. His chaotic and unpredictable nature makes him a great character to explore in fanfiction. Writers can come up with all kinds of crazy scenarios for him. Harley Quinn is also very popular. Her relationship with the Joker and her own journey of self - discovery are often the focus of fanfictions. Another popular one is Bane. His physical strength and strategic mind are interesting to write about, especially in battles against Batman. And then there's Catwoman, who has that alluring and complex personality that draws in readers and writers alike.
One interesting concept could be exploring the backstories of the villains in more depth. For example, in some fanfictions, they might delve into how the Joker became the deranged criminal he is, perhaps giving him a more tragic origin story that makes the reader sympathize with him to a certain extent. Another concept could be alternate universes where the villains team up in unexpected ways. Maybe in one such story, the Penguin and Catwoman form an alliance not just for personal gain but to take on a greater threat in Gotham. Also, there could be fanfictions that focus on the psychological battles between Batman and his villains, like a mind - game where the Riddler challenges Batman in a more complex and cerebral way than in the original comics.
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.