One idea could be a Jedi and a clone trooper swapping bodies. The Jedi suddenly has to deal with the military discipline and combat training of a trooper, while the clone gets to experience the Force and Jedi teachings. For example, the Jedi in the clone's body might struggle with following direct orders without question at first, and the clone in the Jedi's body could be overwhelmed by the newfound connection to the Force.
A great plot for Star Wars The Clone Wars fanfiction could be centered around a new, unknown planet that gets caught in the middle of the war. The planet has its own unique species and culture. The story could follow how the clone troopers and the Jedi interact with this new civilization, whether they try to protect it or use it for their own strategic advantages. Or perhaps a story where a group of clone troopers start to develop their own individual personalities and question their loyalty to the Republic due to some unethical orders they receive. This could lead to a conflict within the clone ranks and force the Jedi to take sides.
A great plot idea would be to have a story centered around a group of younglings who are accidentally caught in the crossfire of a Clone Wars battle. They have to rely on their basic Jedi training and the help of some friendly clone troopers to survive. As they journey through the war - torn landscape, they grow and learn more about the reality of the war. Also, a story about a Separatist scientist who has a change of heart and tries to defect to the Republic with valuable information about new droid technology could be really interesting. He has to avoid being hunted down by his former allies while trying to make his way to the Republic lines.
One interesting plot idea could be exploring the backstory of the Ones on Mortis in more detail. Maybe a young Jedi discovers a hidden prophecy about Mortis and goes on a quest to understand it. This could involve facing challenges related to the balance of the Force that Mortis represents.
A great plot might be Katooni having to deal with a dark side - influenced Jedi who has turned against the Order. She has to find a way to either bring this Jedi back to the light or stop them from causing too much harm. Also, perhaps a story where she discovers an ancient Jedi artifact that holds the key to a great power, and she has to protect it from both the Separatists and those within the Republic who might misuse it.
A plot idea could be a story from the perspective of a minor character during the 'Deception' events. Say, a civilian on Coruscant who witnesses some of the events unfold but misinterprets them. This could lead to a whole chain of events where their false assumptions create new problems or solutions in the Star Wars universe. Also, a plot could revolve around a Sith trying to use the deception for their own gain, but getting caught in a web of their own making.
One interesting plot idea could be Revan emerging from the past and influencing the events of the Clone Wars in unexpected ways. For example, he might have knowledge of a hidden Sith plot that could change the course of the war. Another could be Revan training a new group of Jedi or even influencing Anakin Skywalker's path, perhaps trying to prevent his fall to the Dark Side.
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 plot idea could be exploring her relationship with her clone troopers in more depth. Maybe there's a mission where they have to rely on each other in an unexpected way. Another could be a story about her training a young Jedi padawan during the Clone Wars, showing her teaching methods and how she imparts the Jedi values.
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.
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.