One idea could be creating an OC who is a Jedi with a unique lightsaber form that combines different traditional forms in unexpected ways. For example, a form that mixes Ataru's acrobatics with Makashi's precision. Another idea is an OC bounty hunter who has a moral code that often puts them at odds with other bounty hunters in the Clone Wars universe. They might refuse certain jobs that involve excessive violence or harm to innocents. Also, an OC clone trooper with a special talent like being an amazing artist, using the limited resources on the battlefield to create art that gives hope and a sense of normalcy to his fellow troopers.
Well, you could have an OC that is a smuggler who gets caught up in the Clone Wars. They might start off just trying to make a profit but end up having to choose sides. Or an OC who is a medical droid technician, and through their work, they discover a new way to heal clone troopers faster. Also, an OC who is a youngling that has to go on a secret mission during the Clone Wars to protect an important Jedi artifact.
She could be a clone who rebels against the clone programming. Instead of blindly following orders, she starts to question the morality of the Clone Wars. She might try to find a way to end the war peacefully, even if it means going against her own side. This would create a lot of internal conflict as well as external conflict with her superiors and comrades.
One interesting plot idea could be exploring Dooku's early days in the Sith. Maybe showing how he was gradually corrupted by Sidious. Another could be a story where Dooku has a change of heart briefly and tries to make amends in some small way during the Clone Wars, but is quickly pulled back into the dark side by Sidious' influence. A third idea could be a fanfic that focuses on Dooku's relationship with his former Jedi colleagues during the Clone Wars, like how he feels when facing them in battle.
Another interesting angle would be to have a Clone Wars character, like Anakin Skywalker, land on Earth for some reason. His presence could cause a stir among the people, and his Jedi powers would be both fascinating and potentially terrifying to the Earth population.
One idea could be exploring the backstories of the clone troopers in more detail. Maybe focus on a particular clone and his relationships with his brothers. Another could be creating a new adventure for Anakin Skywalker during the Clone Wars that wasn't shown in the original series. For example, he could be sent on a secret mission to a planet that has a powerful and ancient Sith artifact.
One idea could be focusing on a young clone trooper who discovers he has unique Force abilities. He then has to hide this from his superiors while trying to figure out what it means.
A possible story idea could be that your OC Sith discovers an ancient Sith prophecy. They believe it will lead them to ultimate power. So, they start a quest to find the artifacts related to this prophecy during the Clone Wars. This could involve them infiltrating Jedi strongholds and causing chaos.
One idea could be to focus on Captain Fordo's leadership during a crucial battle in the Clone Wars. Show how he strategizes and inspires his clone troopers.
One idea could be creating an OC who is a lost Jedi from an ancient order. They could have unique Force powers that were long forgotten. Another is an OC who is a smuggler with a heart of gold, getting involved in the Rebel Alliance's affairs by accident.
One idea could be a crossover where Thor somehow ends up in the Star Wars universe during the Clone Wars. Maybe he's on a mission from Asgard to find a powerful artifact that has been lost in this strange new galaxy. He could team up with the Jedi, and his god - like powers would be a huge asset in the battles against the Separatists.