The most exciting plot idea could be a love triangle involving characters from both shows. Picture Dean falling for a female vampire from Vampire Diaries while she also has feelings for a local Mystic Falls guy. Or perhaps an angel from Supernatural, like Gabriel, decides to play some tricks in Mystic Falls and gets involved in the power struggles between the vampires, werewolves and witches there. Another possibility is that the Colt from Supernatural could end up in the hands of a Vampire Diaries character, and everyone is after it for different reasons.
One interesting plot idea could be a battle between the hunters from Supernatural and the vampires from Vampire Diaries. Maybe the Winchesters end up in Mystic Falls and think all the vampires there need to be hunted. Another idea is a character swap. For example, Castiel could end up in the Vampire Diaries world and interact with the characters there in a very different way compared to his usual interactions in Supernatural. A third idea could be a joint mission to fight a greater evil that threatens both universes, like an ancient demon that wants to use the power of the vampires in Vampire Diaries and the magic from Supernatural for its own dark purposes.
Imagine if Elena Gilbert was somehow connected to an Infinity Stone. This would draw the attention of Thanos, but also the Avengers. The Vampire Diaries characters would have to protect Elena while also dealing with the fact that the Avengers are now in their small town. There could be a lot of mistrust at first, but as they learn more about each other's motives and capabilities, they form an alliance to keep the Infinity Stone out of Thanos' hands.
Well, perhaps Hermione is sent to the 'Vampire Diaries' world to retrieve a powerful magical artifact that has somehow ended up there. Along the way, she meets Damon and Stefan. She forms an unlikely friendship with them as they help her search for the artifact. In return, she uses her magic to protect them from some of the more dangerous supernatural threats in their world.
One idea could be that some of the Glee characters visit Mystic Falls for a singing competition. While there, they get caught up in the vampire drama. Maybe a vampire takes a liking to Rachel's voice and wants to turn her into a vampire so she can sing forever. Another plot could involve the vampires using the Glee club as a cover to hunt during their events.
One common trope is the 'fish - out - of - water' situation. For example, when the characters from Supernatural first arrive in Mystic Falls, they are confused by the different rules of the vampire society there compared to the monsters they usually hunt. Another trope is the 'power - struggle'. This could be between the powerful vampires like the Originals in Vampire Diaries and the angels or demons from Supernatural. They often have to compete or cooperate depending on the situation in the fanfic.
The clash of powers. Naruto's chakra - based jutsu against the vampires' superhuman abilities like speed and compulsion. It makes for some exciting battle scenes.
A really interesting plot twist is when a character from Arrow gets turned into a vampire in some fanfictions. For example, in 'The Dark Transformation', Felicity Smoak gets bitten by a vampire and has to deal with her newfound vampiric nature while still trying to help Team Arrow. It completely changes her character dynamics and adds a whole new layer of complexity to the story.
One interesting plot idea could be that Fem Naruto, with her ninja skills, enters the Twilight world. She might get involved in the vampire - werewolf conflict. For example, her ability to sense danger could be a great asset. Another idea is a love triangle between Fem Naruto, Edward, and Jacob. Her strong - willed nature would add a new dynamic to the relationship.
Perhaps a plot where the Persona characters are invited to a special tournament in the Senran Kagura world. The tournament has strange rules that are different from what they are used to. As they participate, they start to notice some dark undercurrents. It turns out that an enemy is using the tournament to drain the energy of the combatants for a nefarious plan. The Senran Kagura and Persona characters must then put aside their differences and work together. The Persona characters can use their Personas to analyze the situation and the Senran Kagura characters can use their combat expertise to fight the physical battles.
One interesting plot idea could be the combination of the technology from Mass Effect and the world - building of Anthem. For example, Shepard could find himself in the world of Anthem and have to adapt to the javelin exosuits while also dealing with the local threats. Maybe the Reapers start to target the world of Anthem as well, and the two groups from different universes have to team up to fight this common enemy.
One idea could be that the Hogwarts students are sent to Mystic Falls for a magical exchange program. Harry could meet Elena and they discover a new dark magic that is related to both the wizarding world and the vampires. Another could be that a vampire from Vampire Diaries somehow ends up at Hogwarts and has to navigate the magical rules and classes while hiding their true nature from most students. A third idea is that the Death Eaters team up with some of the bad vampires in Vampire Diaries to create chaos in both worlds.