I've tried both options. Having them as separate ships helps for following waypoints properly, results in fewer problems with the time-to-completion thing (with single ships, I use a 75m distance check for departure cues, not are-waypoints-done-delay), and allows all the ships to travel at top speed, but poses problems when you want a fighter wing to attack or defend the transport/freighter/cruiser/whatever wing. You have to give multiple orders to guard or attack various ships in the formation, rather than simply telling them to attack or guard Omega wing. When you wing them together, they stick to their own formation, limit speeds, and have the waypoints problem, but the later can be solved by the final-waypoint-1000m-after-departure-cue-fires method. I use the later for the most part, though some changes such as those suggested would be welcome.