It could be Pikachu. Pikachu is a very popular Pokémon and it's not a legendary. It might get tired of seeing the legendaries always in the spotlight and decide to lead the rebellion. Another possibility is Charizard. Charizard is strong and has a bit of a rebellious streak already, so it would make sense for it to be involved in something like this.
Well, it could be about a group of regular Pokémon who are tired of being overshadowed by the legendary Pokémon. Maybe they start to form an alliance to demand equal treatment, like access to better habitats or more respect from trainers. They might use their unique skills in ways that the legendaries haven't expected, creating a whole new dynamic in the Pokémon world.
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.
Hermione could be one of his allies. Despite her usually rule - following nature, she might side with Harry if she sees the merit in his rebellion. Also, Ron would likely be there, as he has always been by Harry's side through thick and thin.
In such a fanfic, perhaps Harry might rebel because he feels the Order is being too overprotective. He could think they are holding him back from fully exploring his power to defeat Voldemort. For example, they might not let him go on certain dangerous missions he believes are crucial.
Maybe an older priest who has a long - time companion Pokemon, like a Growlithe. He uses his experience with both the church and Pokemon to guide the younger members of the congregation, especially those who are also trainers. He helps them see how their Pokemon can be a part of their faith and not just for battling or collecting.
The main character could be a young trainer named Ash. He's always eager to learn more about Pokemon and is very friendly. Another character could be Misty, a girl who is really good with water - type Pokemon and is a bit of a tomboy. There could also be Brock, who is knowledgeable about Pokemon care and often gives advice to other students.
Ezra would likely be one of the main characters. He's always at the forefront of the Rebels' adventures.
Avalanche members could be the main characters. They are already against Shinra's actions in the original story, so it's likely they would be at the forefront of a coup. Barret, with his strong will and leadership skills, could be leading the charge. Tifa, with her combat abilities and loyalty, would be a crucial member. Cloud, with his superhuman strength and his own vendetta against Shinra, would also play a major role.
A young trainer from an underdog region who rises to be a leader in the war effort. He or she could have a unique bond with a Pokemon that gives them an edge in battles.
Another possibility for main characters could be Rainbow Dash from MLP and Blastoise from Pokemon. Rainbow Dash is brave and loves adventures, which would be perfect for exploring the new Pokemon world. Blastoise is strong and reliable. They could form a great team, with Rainbow Dash using her speed to scout ahead and Blastoise using its water attacks to protect them from danger.