A group of clones could start a comedy improv troupe to boost morale. They perform skits that are parodies of their generals and the various alien species they encounter. This gets the attention of some Sith Lords who are initially confused by the strange behavior but then find themselves secretly enjoying the shows.
One of the funniest Clone Wars fanfictions could be about a clone trooper who has an unexpected talent for cooking. He tries to introduce his unique recipes to his fellow troopers, leading to some chaotic and hilarious mess hall scenes.
Another fanfiction concept could involve Jedi and Sith being reincarnated on Earth. They'd have to adapt to modern society while still holding onto their powers and the eternal struggle between the light and dark side. For example, a young Jedi might discover their powers in a world full of distractions and temptations, and they'd have to learn how to use them for good.
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.
One plot idea could be that the OC is a secret agent working for the Republic and is assigned to protect Riyo Chuchi during a crucial diplomatic mission. Along the way, they face attacks from Separatist assassins and have to use their wits and skills to keep her safe.
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.
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.
One idea could be that Naruto is somehow transported to the Star Wars universe during the Clone Wars. He could use his ninja skills, like his shadow clone jutsu, in unique ways on the battlefields. For example, his clones could be used to create diversions while the Jedi try to outmaneuver the Separatist droids.
Perhaps a fanfiction where some of the Naruto characters are actually clones themselves, like in The Clone Wars. Naruto could be a special clone created with a combination of chakra and the Force. His purpose could be to bring peace between the two universes. Hinata could be a healer in this new world, using her gentle nature and Byakugan to sense injuries and use the Force to heal them. This would mix the two universes in a unique way and create a lot of new storylines.
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.
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.