I played a game today where we had Squadrons "docked" in the bays of their motherships. Ships could have more than their squadron value aboard if the player wanted. We've toyed with the idea of having squadrons dock with a capital ship mid-game to receive repairs, but most games don't run that long. Anyway, here's a rundown of what we did.
Any docked squadrons were placed on or near the ship card of the mothership at the beginning of the game. Those squadrons could not be attacked.
When a ship revealed a squadron command, it could activate squadrons on the table, or place a number of berthed squadrons in base contact and then activate them.
While I understand that not everyone wants to do this, it was a blast! It made bombing runs a little more effective, and made keeping an effective combat air patrol an essential part of maneuvering. After all, you didn't want to get caught without any interceptors around your Star Destroyer when the Frigate launched three squadrons of B-Wings at you!