Giovanni is usually a main character. He's the leader of Team Rocket and in the Rainbow Rocket scenario, he's a central figure. Lysandre from Team Flare could also be a main character. His extreme views and his connection to the Rainbow Rocket's overall plan make him important. And of course, the protagonist of the fanfic, who could be a young trainer trying to stop their evil plans.
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.
In a Pokemon Red join Team Rocket fanfic, the main character could be a disillusioned trainer. Maybe they've lost a few too many battles and are looking for a new way to gain an edge. Team Rocket seems like an alluring option. They join up and are immediately thrust into the world of illegal Pokemon trading. However, they soon meet a friendly Pokemon that shows them kindness despite their new allegiance. This makes them question their decision to join Team Rocket and they start to think about how they can use their new position to actually help the Pokemon instead of harming them.
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.
One idea could be exploring the backstories of the Rainbow Rocket members in more detail. For example, Giovanni's motives and how he assembled the team. Another could be a scenario where the protagonist has to infiltrate the Rainbow Rocket base. Maybe they have to find a way to stop a new, more powerful weapon the team is developing.
One interesting Pokemon Team Rocket fanfiction could be about a Team Rocket member who has a change of heart. For example, they might start to see the beauty in the relationship between trainers and their Pokemon and decide to secretly help the heroes instead of causing trouble.
Jesse and James from Team Rocket are always interesting. Their use of hypnosis adds a new layer to their already complex characters. They become more menacing when they can hypnotize their opponents. Also, Ash can be an interesting character in this context. His determination to break free from hypnosis or protect his Pokemon from it shows his strong will. And Pikachu too. Imagine Pikachu trying to fight off the effects of hypnosis while still being its cute and powerful self.
One common theme is the power struggle. Team Rocket uses hypnosis as a tool to gain an upper hand in their devious plans against Ash and his friends. For example, they might try to hypnotize Pikachu to steal it. Another theme could be the moral dilemma. The characters who are hypnotized often face a battle between their true selves and the commands implanted by the hypnosis. It also often features the idea of breaking free from the hypnosis, showing the strength of the bond between Pokemon and their trainers.
Well, it could make for a really interesting fanfiction. Dawn joining Team Rocket would change the whole dynamic. Her Pokémon might not be too happy about it at first. She could bring new ideas to Team Rocket, since she has a different way of thinking compared to Jessie, James and Meowth. However, it's also possible that she would secretly be working against Team Rocket from the inside, trying to take them down while pretending to be one of them.
One thing that would happen is that his Pokémon battles would take on a whole new meaning. Instead of battling for the sake of becoming a Pokémon master, he might be battling to further Team Rocket's goals. His Pokémon would have to adjust to this new purpose. Also, Ash would probably have to wear Team Rocket's uniform, which would be a really strange sight for fans who are used to seeing him in his normal get - up.