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.
One possible plot could be that Daredevil and Batman are both on the hunt for a new criminal mastermind in Gotham. This criminal has a unique way of operating that blurs the line between legal and illegal in a way that challenges both of their moral compasses. They initially clash due to their different methods, but then realize they need to work together to take down this new threat.
Ra's al Ghul would be a fascinating villain in a crossover. He has a global view of crime and destruction, and his Lazarus Pit gives him a certain immortality. His plans could involve both Hell's Kitchen and Gotham in some grand scheme. Daredevil would be out of his depth dealing with Ra's al Ghul's long - term, world - changing plans, and Batman would have to bring Daredevil up to speed while also trying to stop Ra's al Ghul's latest plot.
Well, perhaps a plot where a powerful and mysterious villain frames both Batman and Daredevil for crimes they didn't commit. They have to work together to clear their names while also dealing with the chaos the false accusations are causing in their respective cities. Batman uses his resources and intellect, and Daredevil uses his street - level knowledge and fighting skills to uncover the real culprit.
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.
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.
Jigsaw could also work well. His insanity and penchant for creating chaos would be a big threat to both Daredevil and Jessica Jones. He could be targeting people in both of their circles, leaving a trail of mayhem that they have to follow. His unpredictable nature would add an element of danger and keep the story tense as they try to figure out his next move.
It could be the Joker. Imagine the Joker getting involved in a global scheme and teaming up with some international bad guys. His chaotic nature would be a huge challenge for both Batman and the Totally Spies. He would use his usual tricks like laughing gas and mind games, but on a much larger scale.
Batman is very much a loner who plans everything meticulously. Daredevil, on the other hand, is more impulsive and often dives right into situations. Their different approaches would likely cause clashes. For example, Batman would want to spend time researching and setting up a trap for a villain, while Daredevil might just want to go after the bad guy immediately.
One possible plot could be that a new super - villain emerges in Gotham who has the ability to manipulate sound and light in ways that can disrupt both Batman's high - tech gadgets and Daredevil's enhanced senses. Batman and Daredevil initially clash due to their different methods of dealing with crime, but then realize they need to work together to stop this villain. They could combine Batman's detective skills and resources with Daredevil's street - level fighting and intuition to track down the villain's lair and defeat him.
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.