I love this mod, makes life so much better.

Anyway, one thing that happens is I get "lost" when the ground is just cleared map and the mini map is just the same bare ground - I have a lot of that right now -> http://i.imgur.com/BP23EVN.png

So a waypoint indicator icon would be very helpful. Even if it was just an arrow that pointed to your spawn point, and even then was just pointing either N, NW, W, SW, S, SE, E or NE to save on having to do fancy animations or drawings.

Obviously more sophisticated would be better, such as multi points and colors etc. but that would need loads of UI.

Looking at that map, I can see why you like the mod :D
It's a neat idea for a separate mod, which I imagine wouldn't be difficult to do. I think you will find however that the next update is quite useful for your case, because it will allow you to auto-fly to designated heli pads and possibly map coordinates.