The plot should be engaging and make sense. It can't just be a random mash - up. A good Gotham crossover fanfiction will have a plot that ties the two (or more) universes together in a logical way. Maybe there's a common threat that forces the characters to work together, like a super - villain that exists in both universes and the characters from Gotham and the other crossover property have to find a way to stop it.
It could be amazing. Imagine Clark Kent from Smallville finding himself in the dark and gritty Gotham. He might use his powers to help Batman clean up the city in a different way. Their different moral compasses could lead to some interesting interactions, like Clark's more idealistic view clashing with Batman's darker pragmatism.
One possible plot could be Naruto being transported to Gotham. He might initially be confused by the dark and crime - ridden city. But with his ninja skills, he could start to fight crime in his own unique way, perhaps using his shadow clones to patrol different areas of Gotham simultaneously. His positive and determined attitude could also inspire some of the more down - trodden citizens of Gotham, like the orphans in the city.
Well, Fanfiction.net is also a great place to look for Gotham crossover fanfiction. You might find crossovers with other DC properties. Some writers like to cross Gotham with the main DC universe, creating scenarios where the Gotham version of the characters meets the more traditional comic - book versions. It adds a new layer of complexity and fun to the stories.
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.
Lex Luthor would see Gotham as a new playground. He could try to manipulate some of the power players in Gotham, like the mob bosses or corrupt politicians. Batman would be on to him quickly, though. And this would lead to a cat - and - mouse game between Lex and Batman. Meanwhile, Clark would be caught in the middle, trying to figure out who to trust and how to stop Lex without causing too much collateral damage.
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.
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.
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.
Maybe there's a meta - human or a super - villain who is causing chaos in both cities. Batman is too occupied with Gotham's internal affairs, so Arrow comes to help. They discover that the villain has a base in an abandoned area between the two cities. They have to combine their resources, like Arrow's high - tech arrows and Batman's detective skills (even if Batman himself isn't directly involved but his influence on Gotham's crime - fighting is there), to take down the bad guy.