My suggestion to make the game have a change in pace and have more strategies with PvP and PvE:
A Carrier based ship that utilizes fighters/bombers, but it can't use main weapons.
The carrier can rebuild the fighters/bombers after a cool down that is decreased by each carrier level, but the cool down increases with each level the fighter/bombers are upgraded (got to make things balanced right?). The fighters can be rebuilt faster than the bombers.
Fighter/Bombers with appropriate modules for their roles. Ex: fighters can be equipped with lasers/cannons-(higher damage but slow firing) and bombers can be equipped with missles/torpedoes-(higher damage but slow firing).
Another module for the fighters/bombers that can be equipped are shields with reduced hitpoints.
The number of fighter/bombers that can be on a carrier MAY increase based on the level of the carrier. The max number can be determined by the users. The carrier can start with a capacity of 1.