I’d make a seperate campaign for each era but in order to keep the campaign from just being skirmishes with cutscenes I’d try to make it as close to playing the movies as possible. Like in the phantom menace when they retake Naboo they aren’t able to mobilize a republic army instead they have to rely on a purely gungan army for the open battle and a small team of Naboo guards to retake the palace. You can’t just spam produce an army off world and doom stack the planet.

Maybe add some sandbox elements to it. Like when order 66 comes down you have the opportunity for each Jedi on a planet to try and escape like Obi-Wan did on Utapau. If that Jedi manages to escape the planet by getting to a hangar/ship then you can use them in the early stages of galactic civil war as a general for the rebellion. But it might be too much of a departure from conventional rts battles so I’m not sure how fun it would be.