I had this idea back in beta, but I totally forgot about it!
The way I wanted it to work:

Ok.
Red - Rallypoints
Blue - Team Grunts
Orange - Neutral Grunts
Yellow - End Points
I think you team should be able to drag the corners of these paths to other rallypoints. It should take effect the NEXT grunt wave.
Which would allow you to swap where they all go VERY easily. You have to end at the citidel obviously. And you have to have paths TO the rallypoints.
Hell, you could even do this...

Obviously only 1 team shown to prevent confusion...but you see what I mean.
I think it should use the SupCom move command look.
You know, this.
What do you think?