It might be nice to have advanced assignments like this unlocked by the Leadership skill tree.
What if all things were unlocked by the leadership skill tree, something like a "command" skill or something?
Level 1 would activate the combat commands (harrass, strike, etc.); Level 5 would unlock the advanced waypoint commands (assemble Civilian, assemble carrier, recon); Level 10 would allow you to transfer command.
You would have the basics, like "defend waypoint", "engage" and stuff like that, but you would need the skill for more complex commands.
I haven't played in ages, so I can't remember all of the names of the commands.