A new, self - made villain who is obsessed with colors and wants to collect all the 'powerful' colors in the world. Robin's red stands out to him as one of the most important ones to obtain, so he sets out to defeat Robin and take his red essence.
Maybe the main antagonist is an old enemy of Robin's who becomes jealous of his new powers. This enemy then devises a plan to steal Robin's powers or at least neutralize them so that he can regain his former status as the top threat. He could be a powerful martial artist or a criminal mastermind with a large network of henchmen.
The main antagonist could be a deranged chemist who was once shunned by the scientific community. He uses his knowledge of chemistry to create deadly toxins and gases to get revenge on those who wronged him. He sees Batman and Robin as obstacles in his path of destruction.
It could be a jealous rival. Maybe someone who has always been envious of Robin's abilities or popularity. Now that Robin is in a more vulnerable state as a girl, this rival sees an opportunity to undermine him.
Perhaps a stray dog. The dog is always looking for something to chase or bother. When it sees the mommy cat taking care of the baby robin, it decides to make trouble. It tries to scare the cat away from the robin so that it can have fun chasing the small, helpless bird.
It could be a new villain who has a grudge against the Justice League. Maybe someone whose family was affected by the League's actions in the past. This villain would be very smart and powerful, creating elaborate traps for the League members.
Perhaps a powerful sorceress. She could be jealous of Robin's connection to Batman and the other heroes, so she uses her magic to turn Robin into a girl as a way to humiliate and weaken him. The sorceress could then try to use Robin's new form to her advantage, like trying to make Robin turn against the heroes or something.
Lex Luthor could be a great main antagonist. He could be jealous of the trio's popularity and see them as a threat to his own power - hungry plans. He might create elaborate traps and use his vast resources and intellect to try and take them down, all while trying to make it look like they are the bad guys in the public eye.
The Riddler could be a great antagonist. He might have a grand scheme that not only affects Gotham but also has implications for the Justice League's interests. His riddles could stump both Robin and the League members, forcing them to work together to decipher his plans.
A new, original character could be created as the antagonist. Maybe a powerful and vengeful assassin who has a grudge against Robin for some past event. This character could have unique abilities and a personal vendetta that drives the conflict in the fanfiction.
The Riddler could be a great antagonist. He could set up puzzles and traps all over the city that is now Robin's jungle gym. Robin would have to solve the riddles to avoid the traps while still using the urban jungle gym to his advantage.