The only time that I think flying in a actual ship would be if you had to go destroy a über juggernaut. Like, A HUGE (notice the caps lock) ship that is so large that a few dozen Terran destroyers could fit in it (like, not in theory, but with enough enough free space for them to go fit inside). And rather then sending in hundreds of ships to uselessly get swatted by it, rather send in a few fighters and bombers to destroy the reactor from the inside. And by scripting cause that to make the ship to go *BOOM*. Like, it would be fun to go and have a dogfight 'in' a ship, but if everything from destroyers up had these massive fighter bays that you could actually go in and be concealed, it would make everything kinda cheap.