So, i was thinking. IMO the perfect place to have something like this is in the role select screen. You select your plane, and next to the briefing button, when you are getting ready to jump into pit, add a button that says "Waypoints". You click it and you get a view of the map where you can designate your waypoints. You confirm in that screen, go to the pit and fly away.
I admire heatblurs method of allowing you to change on the fly, but interface wise, you really dont need anything more complicated than what I just mentioned.
Surely this is something that can be addressed relatively quickly? Its a huge core feature.