Would be cool having a special carrier that has the ability to have the player remote control a fighter, could be a special kind of fighter, a frigate sized one that can only be equipped by carriers using a special hullmod, or with an insanely high cost.
The end result would be the player still using a capital class ship as flagship, thus having the bonus related to that, and strategically taking control of the frigate to chase smaller enemies or get behind big ones, which seems pretty fun gameplay. Also having a frigate with CR/hull/armor that can be replenished by the mothership, thus useful in prolonged fights, at a high cost of course, since you have to bring a whole carrier dedicated for that, that might not be as strong as other carriers.
Basically you trade direct mass fighter power with fun and tactics.