A completely new villain created specifically for the crossover could be interesting. This villain could have the power to manipulate the speed force in a way that no one has seen before, and Kid Flash would have to figure out how to stop this new threat while also dealing with the changes in the world due to the crossover.
Zoom could also work well. His speed - stealing powers could pose a major threat to Kid Flash, especially if in a crossover setting he manages to gain new powers or allies. Maybe he teams up with a powerful magic - user from another series to try and finally defeat Kid Flash once and for all.
The Reverse - Flash would be a great antagonist. His time - traveling abilities and his vendetta against the Flash family could make for a really intense story, especially if he teams up with other villains from the Kid Flash's universe in a crossover.
The Riddler could be a great main antagonist. He could create puzzles and traps that are based on both the Flash's speed and Gotham's dark secrets. For example, he might set up a trap where the Flash has to run through a maze of moving walls in Gotham while also solving riddles that are related to Batman's past.
Darth Vader could be a great main antagonist. His power in the Force and his imposing presence would be a huge threat to The Flash. He could try to capture The Flash to study his speed abilities for the Empire.
Perhaps a rogue demigod who has made a deal with a speed - based meta - human villain from the Flash's world. Together, they plan to take over both the magical realm and Central City. The demigod could use his powers in combination with the meta - human's technology to create some really tough challenges for Percy and the Flash.
The Reach could be a great antagonist. They might see Kid Flash's return as a threat to their plans for Earth. They could try to capture him and study his powers to find a way to counter the other heroes. Since they are an alien race with advanced technology and devious plans, they would pose a significant challenge for the 'Young Justice' team.
The Riddler could be a great main antagonist. He could use his intellect to create puzzles and traps that not only challenge Batman's detective skills but also the Flash's speed. For example, he could set up a series of time - locked puzzles where the Flash has to use his speed in a very specific way at specific times to unlock them, while Batman has to figure out the overall pattern of the puzzles.
It could be a bully in the village. This bully could constantly pick on Naruto because of his status as the Jinchuriki of the Nine - Tails. He might try to steal Naruto's food or prevent him from playing with other kids.
It could be a time - traveling villain. Since the story involves watching the future, a villain who can manipulate time would be a great fit. This villain could be trying to change the future for his own evil purposes, and The Flash has to stop him to preserve the good future.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
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.
A new meta - human villain created specifically for the crossover could be interesting. This villain could have the power to control shadows and use them to move quickly, mimicking the Flash's speed in a way. In Gotham, he could use the city's many dark corners and alleys to his advantage. He could also be a master of disguise, fooling both the Flash and Batman. His motives could be to take over both Gotham and Central City and create a new world order where meta - humans rule over normal humans.