Padmé. In the prequels, she had a lot of potential that wasn't fully explored. You could develop her political skills more, show how she really influenced the Senate's decisions. Also, Count Dooku. His reasons for turning to the Dark Side could be explored in more depth. Maybe there were personal tragedies or ideological differences that drove him.
Well, you could do a 'Star Wars prequels remake fanfiction' that delves deeper into the political intrigue. The prequels had a lot of political aspects, but in a fanfiction, you could make it even more complex. Show more of the Senate's inner workings, how the various factions were really plotting. Also, you could add new alien species into the mix. Maybe there are some species that were secretly influencing the events of the prequels but were never shown. And for the characters, you could give them different personalities. For instance, make Obi - Wan more of a maverick Jedi, not always following the traditional Jedi code to the letter.
Anakin Skywalker is one of the most interesting. His fall from a promising Jedi to Darth Vader is a complex and tragic story. Padmé Amidala is also interesting as she is a strong female character involved in galactic politics and in a doomed relationship with Anakin. And then there's Palpatine, whose slow and devious rise to power is fascinating to follow.
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.
Molly is often overlooked but has great potential. In fanfiction, we could explore more of her relationship with her father and how that affects her role as a Starcatcher. We could also see her develop her own unique magical abilities beyond what's shown in the original story.
It introduced new planets like Naboo, which was a beautiful and important world. It also showed more about the Jedi Order, like their training methods and hierarchy. And the Clone Wars added a whole new dimension to the universe with different clone trooper types and the various Separatist droid armies.
The prequels novels contribute by exploring the relationships between characters in more detail. Like the relationship between Obi - Wan Kenobi and Anakin Skywalker. Novels can show their conversations and interactions that the movies might not have time for.
Ahsoka Tano is a likely character. She was Fulcrum in the Star Wars Rebels series, so fanfictions could center around her adventures as Fulcrum. Her past as Anakin Skywalker's apprentice could add depth to the story.
An old Clone Wars veteran, either a clone or a non - Jedi military figure, could be the main character. They have seen the destruction of Order 66 and now suspect there is more to the story with Order 67. Their knowledge of the past wars and military strategies would be useful in uncovering the truth.
The main characters could be a group of bounty hunters. They get hired to investigate the origin of Order 69, thinking it might lead to a big payday. As they dig deeper, they find themselves in the middle of a galactic conspiracy. There could also be a Sith apprentice who is using the chaos caused by the order to rise in power within the Sith hierarchy.
Even Boba Fett could be a main character. He's used to dealing with dangerous situations. In a zombie - infested Star Wars world, he could be hired to retrieve something from a zombie - filled area. He'd use his weapons and his bounty hunter skills to survive the hordes of undead while also facing other threats in the galaxy.