One common theme is loyalty. You often see clones having to choose between their loyalty to the original clone army programming and their newfound beliefs in the rebellion. Another theme is identity. Clones struggle to define themselves outside of their military roles.
A clone trooper named Rex could be a main character. He's already shown some signs of independent thinking in the official Star Wars lore. Another could be a Jedi who is sympathetic to the clones' cause, like Ahsoka Tano. She has a close relationship with the clones and might be more likely to side with them if they were to rebel. And a third character could be a new clone who has a unique genetic mutation that gives him enhanced abilities and a stronger will to fight for freedom.
One idea could be exploring the lives of clone troopers who start to question their loyalty to the Republic. They might discover some dark secrets about the Jedi or the Senate that make them consider joining a rebellion. Another plot could involve a young padawan who teams up with a group of clones to fight against a new Sith threat that the Jedi Council is unaware of. Maybe a group of clones find an ancient force - related artifact that gives them unique powers and they use it to fight for their own freedom.
Well, there's a fanfic called 'Clone Defectors in the Rebellion'. It tells the story of a small unit of clones who defect to the rebellion side. They bring with them valuable military knowledge and skills that help the rebels in their fight against the Empire. It's really interesting to see how they adapt to the rebel way of life.
In a lot of these fanfictions, Luke Skywalker is often a favorite. He's such a central figure in the Star Wars universe and in the context of the Jedi Rebellion, he represents hope and the revival of the Jedi Order.
One common theme is the fight for freedom. The Rebellion is all about overthrowing the oppressive Empire. Another theme is heroism. The characters in these fanfics often show great courage. And unity is also a theme, as the different members of the Rebellion have to work together.
If Thrawn joined the Rebellion, it could change the way the Rebellion is perceived. His reputation as a fearsome Imperial might make some factions within the Rebellion hesitant, but his skills would eventually win them over. Also, his presence could lead to new alliances as other species and groups see the Rebellion as a more viable option with Thrawn on board.
There are also storylines that focus on individual characters within the Rebellion. For example, how they joined the cause and what they sacrifice for it. These stories help to flesh out the diverse characters in the Star Wars universe during that era.
There could be a group of diverse characters. For example, a pilot who is an excellent flyer but has a bit of a rebel attitude. And a mechanic who is crucial for keeping the ships in working order. They all come together to form the core of the rebellion story.