One idea could be Loki somehow getting transported into the Pokemon world. He could use his trickery to outwit the Team Rocket - like stealing their plans and using them for his own amusement. Maybe he forms an unlikely alliance with a Pikachu that has a mischievous streak similar to his own.
Another story idea is that the Joker somehow gets his hands on a powerful and mischievous Pokemon like Ditto. Ditto can transform into any other Pokemon, and the Joker uses it to create all sorts of mayhem in Gotham. Batman has to figure out how to stop the Joker and his shape - shifting Pokemon while also dealing with other criminals who see this as an opportunity to cause more trouble.
One idea could be Loki getting angry at Thor for constantly overshadowing him in Asgardian affairs. Maybe he feels that Thor is always getting the glory while he is left with the scraps. Another could be Loki being angry at the Avengers for imprisoning him after the New York incident. He might plot elaborate revenge in the fanfic.
Loki would likely interact with Pokemon trainers in a rather devious way. He might trick them into giving up their Pokemon or their valuable items. For example, he could pretend to be a lost traveler in need of help and then when the trainer gets close, he'd pull a fast one on them.
One idea could be a fanfic where a trainer discovers a new and rare Pokemon species in an uncharted region. Another could be a story about a Pokemon that has unique abilities and how it changes the Pokemon battles in a particular area. Maybe a fanfic that focuses on the friendship between a trainer and a Pokemon that is usually considered difficult to train.
Another interesting concept is to write a fanfic about a group of Pokemon that form a secret society. They have their own rules and goals, and the story could follow a human or a Pokemon who stumbles upon this society and gets involved in their affairs.
A great plot could involve a world where Skin Pokemon are the outcasts because their changing abilities are seen as untrustworthy. A group of trainers decides to prove that Skin Pokemon are just as loyal and worthy as any other type. They form a sort of rescue team for Skin Pokemon in danger and work towards changing the perception of these unique creatures in the Pokemon world.
Well, a plot could revolve around Janine being involved in a Pokemon tournament where she uses her unique Poison - type Pokemon in unexpected ways. She might face some opponents who underestimate her because of her small stature but she proves them wrong with her brilliant strategies. Or perhaps a story where Janine discovers an ancient Pokemon artifact that has the power to control all Poison - type Pokemon and she has to protect it from evil forces.
One idea could be that Loki and Deadpool are forced to team up by some cosmic entity. Loki is initially annoyed by Deadpool's constant chatter and antics, but gradually comes to respect his unorthodox fighting style. Another plot could involve Deadpool getting transported to Asgard and causing chaos, with Loki having to either clean up his mess or use it to his advantage. Maybe they could also be on a quest to retrieve a powerful artifact that has been stolen and is being misused in the multiverse.
A plot could involve Loki using his agent skills to manipulate the Avengers into a false sense of security. He then reveals a master plan that involves using their own powers against them to take over Earth. But in the process, he starts to have second thoughts as he gets to know the Avengers better and forms unexpected friendships. For example, his interactions with Black Widow could lead to him seeing the value in human relationships.
One idea could be a story where a trainer is possessed by the spirit of a legendary Pokemon. This possession gives the trainer unique powers and insights into the Pokemon world. They can use these new abilities to face tough challenges and uncover hidden secrets.