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.
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.
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.
One possible plot could be that Misty gets captured by Team Rocket. They plan to use her as a bargaining chip against Ash. But during her captivity, she manages to befriend some of the lower - level Team Rocket grunts. These grunts start to have second thoughts about their evil deeds because of Misty's influence. Eventually, Misty uses this new - found friendship to escape and also cause some internal chaos within Team Rocket.
Misty's Pokemon could be involved in a way where they are all captured by Team Rocket. Then Misty has to rely on her wits and some basic Pokemon - handling skills without her actual Pokemon. She has to find a way to free them. Meanwhile, her Pokemon are trying to communicate with other wild Pokemon in Team Rocket's base to create a sort of uprising. This would lead to a big showdown where Misty and her freed Pokemon take on Team Rocket and their own captured Pokemon.
One common theme is power and control. Team Rocket often tries to brainwash Pokemon or trainers to gain an upper hand in the Pokemon world. Another theme could be redemption. Sometimes the brainwashed characters find a way to break free and redeem themselves. Also, the struggle between good and evil is prominent. The heroes try to stop Team Rocket's brainwashing plans and restore peace.
The main characters might not only be human trainers. Some Pokemon could take on leading roles. For example, a powerful and wise Charizard could be a main character. It might have been trained by a famous trainer in the past but now fights independently against Team Rocket. There could also be a group of Eeveelutions that are the main focus. They have different abilities and personalities, and together they form a force to be reckoned with against Team Rocket. Alongside them, there could be a trainer who acts as a guide or coordinator for their efforts.
Well, the plot might start with a trainer who is a bit of a rebel. They don't like following the normal rules of the Pokemon world. Team Rocket notices this and recruits them. As part of Team Rocket, they participate in raids on Pokemon Centers to steal medicine for their own Pokemon. However, during one of these raids, they encounter a very sick Pokemon that needs that medicine desperately. This makes them question Team Rocket's motives. They then start to secretly work against Team Rocket from within, trying to protect the Pokemon and the integrity of the Pokemon world.
A possible plotline is that some Pokemon start to develop new strategies against Team Rocket. They might learn to communicate better with humans to coordinate attacks. For instance, the Psychic - type Pokemon could use their powers to read the Rockets' minds and share the information with the other Pokemon and trainers. Also, there could be a story where a group of orphaned Pokemon form a resistance against Team Rocket. They have to rely on their wits and natural abilities as they don't have trainers to guide them, making their fight even more heroic.
If Team Rocket turns Ash into a Pokemon, it could lead to a really interesting story. Ash would have to experience the world from a Pokemon's perspective. He'd understand their struggles, like being caught and trained. This could also be a way for him to better understand his own Pokemon and their bond with him. And it would be a wild adventure as he tries to find a way to turn back to his human form.