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.
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.
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.
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.
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.
It's hard to say without reading it, but they could be some original mean - spirited Pokemon trainers or some Pokemon with bad attitudes themselves.
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.
Ash is obviously one of the most popular characters. He's the main character of the Pokemon anime, and in fanfictions, his adventures with or against Team Rocket are always interesting. People like to see how he reacts to different situations that Team Rocket creates or how he manages to outwit them.
Well, if Ash joins Team Rocket in a fanfic, it would be a huge shift in the Pokemon world. His friends, like Misty and Brock, would be shocked. They might try to rescue him. Ash, on the other hand, could initially be attracted to the idea of a new adventure with Team Rocket. He could see them as underdogs in a way, always failing but still trying. But as time goes on, he'd start to see the problems with their way of doing things.
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.
There might be a young and determined trainer as one of the main characters in 'the great pokemon war fanfic'. This trainer could be on a quest to end the war and bring peace. Alongside him or her, there could be a group of unique Pokemon with special powers. There may also be an antagonist, perhaps a power - hungry trainer who started the war in the first place. And perhaps some side characters like a wise old Pokemon professor who gives advice to the main characters during the war.