Auto Pilot Waypoint Option
Currently the auto pilot feature of the Remote Control forces your craft to stop at every waypoint on its journey. This behavior becomes troublesome as ships gain mass because they take on cargo or are just built big. When a heavy ship stops on a dime at a waypoint it takes so much time for the auto pilot to get things going again that many times the craft just sits while the auto pilot continues to cycle through waypoints as if it were still moving. The general fix for this is to turn the auto pilot off after reaching a waypoint, manually accelerating the ship, and then turning the auto pilot back on. This means it is no longer an auto pilot.
The solution, I believe, is to have an option to prevent the auto pilot from stopping completely at a waypoint, and perhaps loosening up the definition of "reaching" a waypoint so that a large ship will aim towards the next waypoint and begin re-accelerating before actually hitting the exact spot of the current waypoint. There might be some variables the player may need to set such as distance to waypoint that would qualify as "reached".
Otherwise, I suppose this sort of thing would have to be handled by a script which could only be executed in "Experimental Mode".