Commander Bly is quite underrated. In fanfiction, you could explore his relationship with Aayla Secura in more depth. Maybe show his internal struggle when Order 66 is given. Another one is Captain Rex's brother, Cody. There's a lot that could be done with his character, like showing his leadership among the clone troopers and how he dealt with the moral dilemmas during the war. And then there's Sugi, the female pirate. She has a great backstory that could be further developed in fanfiction, perhaps her adventures outside of the main Clone Wars battles.
One underrated character is Tera Sinube. He's an old Jedi Master. A fanfiction could focus on his wisdom and how he might have mentored younglings during the Clone Wars in ways different from the more well - known Jedi. Then there's Asajj Ventress' Nightsister clan. While Ventress herself is well - known, the other Nightsisters could be the center of a fanfiction. You could explore their culture, magic, and how they interacted with the events of the Clone Wars. Also, R2 - D2's counterpart on the Separatist side, U9 - C4, could be an interesting character to focus on. Maybe a story about how it views the war differently from R2 - D2 despite being a similar type of droid.
Commander Bly. He doesn't get as much spotlight as some other clone commanders, but he has a lot of potential. His relationship with Aayla Secura could be explored more in fan fiction. Another is Barriss Offee. Before her fall, she had a lot of untapped storylines. And then there's Tiplee. She was a strong female clone commander who could be the center of some great fan - made stories.
Anakin Skywalker is also an interesting character to focus on. His relationship with Obi - Wan is complex, and during the 'Deception' arc, his reaction to his master's supposed turn to the dark side can be explored in depth. How does he balance his loyalty to Obi - Wan with his duty as a Jedi? And how does it affect his own path towards the dark side?
The story of the Nightsisters is underrated. They have a unique culture and powerful magic. Their interaction with Dooku and the Sith shows a different aspect of the power dynamics in the Star Wars universe. It's a story that's filled with mystery and the exploration of a different kind of power that's not just the Force as we typically know it.
One of the most interesting could be a Jedi apprentice who has a unique connection to the Force. This character might be able to communicate with animals in a way that no other Jedi can. Another could be a clone trooper with a hidden artistic talent. He might use his skills to create beautiful murals on the walls of the clone barracks, adding a touch of humanity to the otherwise military - dominated setting. And then there's the mysterious bounty hunter who has a code of honor that sets her apart from the typical mercenaries in the Star Wars universe.
General Pryde is a character that could be interesting in fanfiction. Instead of just being a villain in the movie, you could explore his motives more. Maybe he had some doubts about the First Order's methods but was too afraid to oppose them. Fanfiction could show his internal conflict and what could have happened if he had made different choices.
One possible fem clone OC could be a highly skilled sniper. In fanfiction, she might have unique markings on her armor that distinguish her from the male clones. She could befriend some of the Jedi, like Ahsoka Tano, and together they face various challenges during the Clone Wars.
I really like Clone Trooper Fives. He has a bit of a mischievous streak that could be played up in a funny fanfiction. For example, he could play pranks on his fellow clones by switching their equipment around or making up wild stories about the enemy.
The main characters are typically the rookie Clone Troopers. They are new to the war and still learning the ropes.
Ezra Bridger is often a great character in fanfics. His growth as a Jedi and his role in the Rebellion make for interesting storylines. Writers can explore his connection to the Force in new and exciting ways.
One unique plotline could be a time - travel story. A character goes back in time to the start of the Clone Wars and tries to prevent certain events from happening. Another could be a story where the clones develop their own culture and start to question their purpose. And there's also the plotline where a Jedi falls in love with a Separatist, creating a conflict of loyalty.