A potential plotline could be a group of Naruto characters getting lost in the Star Wars universe and being mistaken for new threats or allies. They might initially be hunted by the Empire but then be discovered by the Rebels. The Naruto characters could use their unique abilities to help the Rebels in battles. Another plotline could be that a Sith Lord discovers the power of chakra and tries to harness it for his own evil purposes. This would force the combined forces of the Jedi and Naruto characters to stop him. Maybe there's a prophecy in the combined universe that foretells of a group of heroes from two different worlds coming together to save the galaxy from a great evil, and our characters from Naruto and Star Wars Rebels are those heroes.
One plotline could involve a Star Wars Rebels character, say Kanan, traveling to the Naruto universe. He could find that the imbalance of the Force there is related to the disruption of chakra. Kanan could then teach some Jedi teachings to Naruto characters about self - control and balance, which they could apply to their chakra usage. Meanwhile, the Naruto characters could show Kanan the power of their ninjutsu and teamwork. Another plot could be centered around a powerful artifact that has the potential to destroy both universes. Characters from Naruto and Star Wars Rebels have to work together to find and protect this artifact from falling into the wrong hands, whether it be a powerful ninja clan or an Imperial warlord.
Maybe Numa stumbles upon a hidden Sith artifact on Lothal. This discovery could put her in danger as both the Empire and some rogue elements within the Rebellion want to get their hands on it. She has to decide what to do with it and who to trust, which would be a great character - building story.
One interesting crossover could be the sharing of jutsu and the Force. For example, a Jedi might learn how to use chakra to enhance their connection to the Force. Maybe a Naruto character could be trained in the ways of the lightsaber, using their ninja skills to create unique fighting styles with it.
A 'Star Wars Rebels Epilogue Fanfiction' might tell the story of how the Rebellion's victory is being commemorated. There could be a grand ceremony on Lothal, with all the main characters in attendance. During this, we could learn more about the characters' inner thoughts and feelings. For instance, Ezra might be reflecting on his time away and how much he has missed his friends. Or, it could show the characters adapting to a more peaceful life. Sabine might find it hard to let go of her warrior ways at first, but gradually learns to embrace a new role in the rebuilding of the galaxy.
One idea could be to have Naruto characters in the Star Wars Rebels universe. For example, Naruto could be a Jedi - like figure with his chakra being similar to the Force. He could use his shadow clone jutsu in battles against the Empire, creating distractions and overwhelming opponents. Sasuke could be a Sith - like character who is initially on the wrong side but later sees the light.
One great Ezra and Sabine fanfic is 'Bonding on Lothal'. It really delves into their relationship during the Rebellion on Lothal. The author does an amazing job of showing how they rely on each other and grow together as characters.
Well, Galen Marek in a Star Wars Rebels fanfic might be a bit of an anachronism at first glance. But if you think about it, the Star Wars universe is vast. He could have been in hiding for years. In the context of Rebels, he could be a force for change. He might be drawn to the Rebellion's cause because of his own experiences with the Empire's cruelty. His presence could also attract unwanted attention from the Empire, leading to some tense moments in the fanfic. For example, the Inquisitors might sense his power and start hunting him, which could then put the Rebels in danger as they try to protect him.
Some Star Wars Rebels time travel fanfics focus on the relationships between the characters. When time travel is involved, characters may interact with their past or future selves. This can lead to some really interesting character development, like Kanan having to come to terms with a future version of Ezra who has changed a great deal due to his time - traveling experiences.
One great Sabine and Ezra fanfic could be one where they go on a secret mission together. It might explore their growing bond as they face challenges. Maybe they have to infiltrate an Imperial base, and along the way, they learn more about each other's pasts. Their different skills, Sabine's artistry and combat skills and Ezra's connection to the Force, would make for an interesting dynamic during the mission.
One similar fanfic could be 'Endless Struggles in the Rebellion'. It also focuses on the hardships that the Star Wars Rebels characters face. Another might be 'Troubled Times for the Ghost Crew' which, like the one you mentioned, likely has the crew dealing with one problem after another. There's also 'Perils of the Rebellion' which would probably have a similar theme of the rebels constantly facing difficulties.
One aspect could be the Rebels' reactions to the complex political situations in the Clone Wars. They might be shocked or inspired by the different alliances and betrayals that took place. It could also show how the Clone Wars era influenced the technology and weaponry available during the Rebels' time, like how the Rebels might see the evolution of starfighters from the Clone Wars to their era.