Maybe the Reverse - Flash. He could somehow cross over into the Percy Jackson world. He'd be a difficult adversary for both Percy and Flash. He could use his negative speed force to slow down Percy's reflexes and disrupt Flash's connection to the speed force. Percy would have to rely on his wits and the power of the sea to fight back, while Flash would have to find a way to overcome the Reverse - Flash's power - draining abilities.
A new villain could be created specifically for the crossover. A being that has the ability to steal powers. It could target Flash's super speed and Percy's demigod powers. This villain could be some kind of dark wizard or an ancient entity that has been awakened by the crossing of the two universes. Flash and Percy would have to figure out its weaknesses and work together to defeat it, which would involve a lot of exploration of both their powers and the new environment they find themselves in.
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.
Well, it could be really exciting. Maybe Percy uses his water - controlling powers to help Flash when he's running through some kind of water - based obstacle during a race. Or Flash could use his super speed to help Percy get to a crucial location in the demigod world quickly, like to retrieve a powerful artifact before the bad guys do.
The Reverse Flash could also be a main villain in this crossover. He travels to the Smallville universe to cause trouble. He might target Clark, thinking that by eliminating him early, he can change the future in his favor. This would force Barry and Clark to work together to stop the Reverse Flash's evil plans.
It could be a powerful mage who wants to use Percy's demigod powers for his own evil plans. This mage might be jealous of Percy's unique abilities and try to control him.
Definitely Yugi and Percy. Yugi is the heart of the Yugioh series with his connection to the Millennium Puzzle and his dueling skills. Percy, on the other hand, is the hero of the Percy Jackson series, a demigod with his own set of powers. They would be the ones to bring the two worlds together and lead their respective groups in any adventure or conflict.
It could be a character who is jealous of the power that could come from combining the two worlds. Maybe a rogue demigod who wants to use Jessie's knowledge of her world's technology and the magic of the Percy Jackson world to rule over both. This character might start causing problems by stealing important artifacts from both worlds to try and build a device that would give them ultimate power.
The Reverse - Flash would be really interesting. He could target both Batman and the Flash. For the Flash, he's a long - time nemesis, but for Batman, he'd be a new and extremely dangerous threat. His ability to manipulate the speed force and time could put Gotham in chaos in ways Batman has never seen before. And he could use his knowledge of the Flash to try and set traps for both heroes.
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.
The main villain could be an ancient Titan who was imprisoned long ago but has now found a way to break free. This Titan could be seeking revenge on the gods and demigods alike, and Percy and his friends would have to stop him before he destroys the world as they know it.