Ship wide shield projector that is as big as a sensor array if not bigger but less powerful than the normal shield projector and needs more power.
Rail-Gun: a weapon that has a longer range and more powerful than the large cannon but it takes up both power cells and ammunition. say a 2:4 ratio (2 being the ammo and 4 being the power cells) or a 1:2 ratio (1 being ammo and 2 being power cells) it should also be affected by the electro-bolt.
Plasma-Cannon: a cannon that uses power cells to create and shoot plasma. say 3 or 4 power cells per shot and is affected by the electro-bolt.
(also i feel like the weapons in general need a range increase)
edit: Also a hangar concept. have a hangar bay that increases in size based on the size of the assigned ship it is meant to hold and have a hangar factory or assembly where the craft for the hangar is put together. an than have the hangar assembly/factory take up a new resource called materials to put the sub-craft together.
you could also use the materials resource as a in combat repair mechanism with repair crews from repair centers taking materials and slowly re-building the ship.
this allows the player to customize their fighters and bombers an corvettes allowing them to bring in additional ships into combat in a single package. they would operate and act like any other ship though so no need for anything special.