Perhaps there are some neutral characters who get caught in the middle of the conflict between the Sith and the Jedi. They could be ordinary people, or they could be some other species in the Star Wars galaxy that are trying to survive the chaos that the Sith Lords bring with their power - hungry ways.
Power and corruption are likely main themes. Sith Lords are often consumed by their pursuit of power, which leads to their corruption.
The Emperor, of course. He is a central figure in the Sith hierarchy. His manipulations and his grand schemes play a major role in the events of the novel. There are also other Sith acolytes and those who oppose the Sith, like some of the Rebel forces. These characters add depth to the story as they either support or fight against the Lords of the Sith. They bring out different aspects of the conflict between the Sith and the rest of the galaxy.
The Sith Lords themselves are main characters, of course.
In Clone Wars fanfiction, Darth Maul stands out. He was initially thought to be dead after 'The Phantom Menace' but his return in Clone Wars brought a new level of danger. His thirst for revenge against Obi - Wan Kenobi and his attempts to regain his former power are common themes. Darth Sidious is also key. His devious plans to create chaos and gain ultimate power are often explored in fanfiction. He was using the Clone Wars as a means to an end, and fan writers love to play with the idea of what his true endgame was.
The obvious main characters would be the protector and the dark lord. But there could also be secondary characters like the dark lord's enemies or the protector's allies.
One of the notable Night Lords in novels is Talos. He is often a central figure, showing the complex nature of the Night Lords. He has his own moral code, albeit a very twisted one compared to most protagonists.
There might be characters like Kai Allard - Liao. He's often involved in important battles and political intrigues. Another could be Victor Steiner - Davion, who is known for his military leadership. And perhaps Katrina Steiner, who plays a role in the power struggles within the factions.
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The four Dark Kings were the Dark King Wen Tai, the Underworld King Zhan Kong, the Evil Sacred King Mo Fan, and the Shadow Descendant King.
Definitely Anakin Skywalker. He's the one who goes through the most drastic change. Then there's Palpatine, the mastermind behind the Sith's plan. Obi - Wan Kenobi, who has to face his former apprentice. And Yoda, the wise Jedi Master who tries to counter the Sith's plot. Also, Padmé, whose love for Anakin is a key factor in the whole drama.