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.
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.
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.
One possibility could be Reverse - Flash. He could be interested in the Miraculous powers and try to steal them for his own evil purposes. He might see the power of the Miraculous as a way to enhance his own speed or gain new abilities.
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.
Reverse - Flash could be really interesting. He could manipulate time in ways that not only affect Flash but also Supergirl. For example, he could go back in time and prevent Supergirl from arriving on Earth, which would change the whole timeline. Flash would then have to convince her to come to Earth again while also dealing with Reverse - Flash.
Kabuto could be a likely villain. He's very intelligent and has a thirst for power. He could use his knowledge of jutsu and his ability to manipulate others to try and steal The Flash's speed force. He might think that by combining it with his own powers and ninja techniques, he could become invincible.