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.
Another plot could be that a villain from the future travels back to the time of Star Wars Rebels to try and eliminate the Rebels before they become a real threat. This creates a lot of action - packed scenes as the Rebels have to figure out who this new enemy is and how to stop them without the knowledge they have in their own time.
One great 'Star Wars Time Travel Fanfic' is 'A New Hope in Time'. It has an interesting plot where the main character goes back in time to the events of the original movie and tries to change things. Another is 'Time Warp in the Galaxy' which features a unique take on time travel mechanics within the Star Wars universe.
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.
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.
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.
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.
One interesting plot idea could be Kanan traveling back to the time before the Jedi Purge. He could try to prevent certain events that led to the downfall of the Jedi Order. Maybe he meets his old master as a young padawan and has to figure out how to interact without changing the future too much.
In a time - travel story, it could be an alternate version of Ezra himself. Maybe Ezra from a different timeline where he turned to the dark side. This dark Ezra would oppose the normal Ezra, seeing his attempts to change things as a threat to his own power and the dark future he has created.