Another idea is that the Pokemon have some of the abilities of the TF2 characters. So, there could be a Pikachu with the Scout's double - jump ability. Or a Snorlax that has the Heavy's strength and can use a 'Mini - Gun' - like attack which is actually just a powerful Tackle. This would create really unique and interesting battles.
A cool plot could be about a group of Pokemon in the Reborn area that are affected by a mysterious energy source. This energy causes them to start transforming into different Pokemon species. A young trainer decides to study this phenomenon and in the process, uncovers a dark secret about a powerful organization that was responsible for releasing this energy. They then have to stop the organization from causing more chaos with the Pokemon transformations.
Well, a plot could involve May finding a magical artifact that accidentally causes TF (transformation) in all the Pokemon in a certain area. As she tries to fix it, she teams up with some of the transformed Pokemon who still retain their intelligence. They go on an adventure to find the source of the magic to reverse the changes. Maybe there's also a sub - plot where May has to prove to some skeptical trainers that these transformed Pokemon are still worthy of care and training.
Well, consider a plot where the trainer catches a Pokemon that has the ability to TF into objects or even other trainers. This could lead to some really comical and confusing situations. For example, it could transform into a Pokeball to avoid being caught by another trainer. It could also transform into a key item in the Pokemon world, like a Master Ball, and the trainer has to figure out how to get it back to its normal form without losing it forever.
In some fanfics, a human character might be transformed into a half - Pokemon, half - human hybrid. This often involves a complex exploration of identity. The character has to deal with not fully belonging to either the human or Pokemon world, and might go on a journey to find their place in this new state of being.
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.
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.
One idea could be that Ash gets transformed into a Pokémon and has to figure out how to communicate with his friends. Another could be that Team Rocket manages to use a new device to transform Pikachu into a different type of Pokémon. Maybe Ash and Team Rocket end up having to team up when a new, more powerful villain emerges who wants to transform all Pokémon into mindless servants.
A possible plot could involve a Pokemon having some sort of connection to the technology in the TF3 world. Maybe a special Pokemon's power can enhance the soldier's weapons or armor. The soldier then has to protect this Pokemon from those who want to use it for evil. And along the way, he discovers new types of Pokemon and forms bonds with them.
One interesting tf pokemon fanfiction could be about a trainer who accidentally transforms into a pokemon. This would lead to a whole new adventure as they have to navigate the pokemon world from a different perspective.
There are fanfictions where Pokemon transform into humans. For example, a Charizard might turn into a human and struggle to adapt to human society while still having its Pokemon instincts. It could be a really cool exploration of the contrast between the two worlds.