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.
Ra's al Ghul could be the main villain. He discovers the existence of the Flash and sees his speed as a valuable asset for his plans. He tries to capture the Flash and use his powers for his own immortality - seeking goals. Ra's al Ghul's knowledge of ancient and mystical arts could pose a great challenge to the Flash, who is used to dealing with more science - based threats. And in Gotham, Ra's al Ghul could use his League of Shadows to create chaos and draw out the Flash and Batman.
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.
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.
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.
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.
In a Gotham Flash crossover fanfiction, perhaps there's a device that disrupts the speed force and it's located in Gotham. The Flash has to go there to fix it. He meets the various characters in Gotham like the Joker, who tries to use the Flash's powers for his own chaos. Meanwhile, Flash has to work with the likes of Gordon and Robin to stop the Joker and repair the device. The different moral compasses of the Gothamites and the Flash could lead to some interesting character interactions.
It could be a speedster from another universe who has come to challenge Flash. This villain might have some unique powers related to speed that Flash has never encountered before, like the ability to steal speed from other objects or people.
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 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.
Perhaps there's a villain in Gotham who has discovered a way to siphon the Flash's speed force. The Flash has to go to Gotham to stop this villain, and in the process, he meets the various characters of Gotham like Gordon and Catwoman. They all have to work together to not only stop the villain from stealing the speed force but also from using it for some evil plan in Gotham.
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.