Oh right. so you'd create some waypoints, then you could assign ships rts style w/o needing to konw the details of what the assignments are.
I'm not sure we're on the same page here. To make it as clear as I can - you could:
1) Create assignments exactly like you do now - i.e., either click on an objective and pick one, or click to create a waypoint and pick one.
2) Select some ships and right-click to create an assignment OR right-click on an existing assignment. So it'll either create an assignment on an objective, create a waypoint
and an assignment, or assign to an existing assignment.
You still need to know the details of what the assignment is because that affects ship behavior. For example, ships assigned to an "intercept" will have tunnel vision with respect to the target, ships assigned to escort have very specific behavior re: keeping formation with the target, etc.
So, it's not like there's two parallel command structures - it's still the same structure as now, but with RTS-like inputs added.
Let me know if this makes sense