I think in order for this to work properly ships would need to move like real aircraft. At the moment ships can strafe sideways and up/down at max speed, so a joystick would give a disadvantage. Maybe if strafing movement became a lot slower (like 10% max speed so it could only be used for parking manouveres) a joystick could be a good way of piloting a ship. Also, it may be a little impractical for flying Titan-class vessels.
Apart from that, I would love to use a joystick to pilot a ship, especially in a dogfight situation.