I believe ATC flow control is designed to keep airports and airways running at maximum capacity (in terms of a/c, not pax). Long-haul flights are slapped with fewer delays because speed restrictions and/or rerouting can be issued enroute as needed. Short flights may be delayed longer because a greater portion of their flight is conducted in the terminal area... no place to go with them besides a holding pattern, which nobody likes. As an aside, ATC is not supposed to give preference to air carriers over general aviation. Sometimes it seems like they do, but this is probably because the carriers have the benefit of dispatchers filing preferred routes and dotting all the i's, etc.
As far as the departure delays go (everyone wanting to leave the same airport at the same time), they are directly related to managing the airborne departure traffic. Sure, the runway might be able to take X departures per minute, but if the terminal area above the airport can't handle X more airplanes, they're going to sit on the ground. And the delay duration would depend on which airspace you needed.
I may not have the whole picture here, so please feel free to shed some more light on this.