The return of an old Batman villain in a new form could be interesting. For example, the Jokerz. They could be led by a new, more menacing Joker - like figure who has a vendetta against Robin for being part of the new - age heroes. They could start causing chaos in Gotham, and Robin would have to figure out their motives and stop them before they destroy the city.
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.
Terry McGinnis could face off against a time - traveling Ra's al Ghul. Ra's al Ghul has always been obsessed with immortality and the betterment of the world through his own extreme means. If he had the power of time travel, he could try to reshape history to his liking, which would put him directly at odds with Batman Beyond. Ra's al Ghul's long - term plans and strategic mind would make for a complex and engaging conflict.
Ra's al Ghul could also be a main villain. He might see the absence of Robin as a sign of weakness in Batman's legacy. He could try to take advantage of this and further his own plans for Gotham, perhaps even trying to recruit Robin for his own purposes if Robin is out on his own.
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.
A good main villain could be Brother Eye. It's a powerful and menacing artificial intelligence. In a crossover, it could have evolved in the future to be even more dangerous. It could pose a threat to both the future world of Batman Beyond and the past era of the Justice League, forcing them to team up to take it down.
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.
Ink could be a great main antagonist. He has the power to manipulate shadows and could use this ability to create chaos in Gotham and beyond. He might target the Justice League and Batman Beyond because they represent order and he wants to spread his own brand of darkness.
How about Ra's al Ghul? He has his own ideas about justice and order that are very different from Batman's. He could see Robin as a potential recruit for his League of Shadows. Ra's al Ghul could manipulate events to make Robin question Batman's methods and try to draw Robin to his side.
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.
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.
The Joker would be a great choice. He could use some new - fangled chemical or device to mind control Batman. Imagine the chaos he could create with a mind - controlled Dark Knight at his beck and call. He might make Batman do really out - of - character things like laughing hysterically while committing crimes.