If you are looking for an interesting gameplay difference between the empire and the rebels it relates to how their fighter squadron structure is set up. While someone already suggested that you treat all fighters as planes that must base at the end of turns, I don't think that is quite right. It certainly fits the Imperial naval doctrine, but one of the major advantages the rebellion had over the empire were its fighters.
I think that TIE fighters should be treated like planes, but X-wings, Y-wings, etc... should be able to act like any other capital ship with proper bonuses and penalties in combat. Early in the rebellion most of the attacks were made up of small, long-range raiding parties of mainly fighters and I think treating them in this way adds real flavor to the different ways the two factions will play. Plus in the early rebellion there were not sufficient capital ships to launch a traditional "carrier based" fighter attack.