Double clicking factories only selects all of the ones of that type on screen. Typically, I would have factories scattered all over the map and with the maximum zoom level would never be able to select all in this manner.

When you hold shift, you can left click and drag the end points of unit movements, and queued buildings. It would be nice to be able to do the same with factory waypoints as this would prevent having to trace the line(s) to the factories then back to the destination(s) to make adjustments.

Control groups is not a viable solution all of the time. Even on tiny maps I would have 4+ rally points, each being fed by multiple factories which chews through control groups especially if you separate air/armories/factories/dread launches etc to maintain build order control.

Almost all factory waypoint moves that I make are small iterative changes to the next node continuing to support the armies as it pushes forward.

Typically the waypoint move would be very small within a single screen frame, and the factory would be out of screen. Tracking back to the factory to make these small iterative changes is inefficient.

The addition of being able to drag/drop the waypoint would not be exclusive of control groups, but would add additional functionality that would reduce micro-management in several common situations.

Reallocating factories to support a different front line is a separate issue which drag/drop would not be suitable for, and are also not be handled well using only control groups. These situations tend to result in additional micro-management.