Meowth in Team Rocket has a sad story mainly because of his unrequited love for a female Meowth. He learned to speak human language in the hope of impressing her, but she still rejected him. This made him feel very sad and lonely, yet he continues his journey with Team Rocket.
One common theme is redemption. Many fanfics explore the idea of Team Rocket members turning over a new leaf. Another theme is power - seeking. Since Team Rocket is always after powerful Pokémon, this often features in fanfics.
Maybe there's a rogue Pokemon trainer. This trainer is jealous of Dawn's skills and the attention she gets. When Dawn joins Team Rocket, this trainer sees it as a chance to expose her as a fraud. He or she then tries to stop Dawn and Team Rocket's activities, thinking that they are up to no good, which they are, but the trainer has his own self - centered motives.
Yes, in some Team Rocket fanfictions, Ash can be depicted in various ways that might involve him having some sort of connection to Pokémon in a different light. Maybe he could be experimented on by Team Rocket to gain Pokémon - like abilities, or be transformed into a Pokémon - like being in a very creative and out - of - the - box fanfiction concept.
Another theme is the clash of good and evil. Bonnie represents the good side with her pure heart, while Team Rocket is the bad guys. Their interactions often play on this dynamic, with Bonnie sometimes trying to reform them or at least understand why they do bad things.
There are fanfictions where Team Rocket actually turns good. They might start helping Ash and his friends instead of causing trouble. This kind of story often has a lot of character development for the Team Rocket members as they learn new values.
Another plotline might involve Ash teaming up with some of the Team Rocket members, perhaps reluctantly at first. They could be forced to work together due to a common threat to both the good guys and the bad guys in the Pokemon universe. This would lead to some interesting character developments for Ash as he has to deal with the not - so - good nature of Team Rocket.
In a fanfiction where Ash joins Team Rocket, it could lead to some really interesting storylines. Ash has a lot of knowledge about Pokémon training that Team Rocket lacks. He could potentially teach them new techniques, but at the same time, his moral compass would be constantly at odds with their devious ways. Maybe he joins them because he's somehow tricked or he has his own secret plan to take them down from the inside. It would be a great opportunity to explore different aspects of his character and how he adapts to this new situation.