The master plan is Chaos.

Moridin wasn't about to give any orders to stop the conflict between the two factions in the Tower, it rendered the AS totally useless.

A very good reason not to kill Egwene too soon is that she was predictable, while her gone the game became a lot more unpredictabe. She's tied to the boys' ta'veren webs. As long as Egwene was around, Moridin could be pretty certain it's through her the Wheel would work to bring the AS together, and then behind Rand in the end. Same for Andor and Elayne. Predictability meant he could place Aran'gar near her, and keep an eye on things, judge when the time comes to strike.

Moridin seems to have seriously miscalculated, believed it would be very easy to eliminate all these people and screw the Wheel at the last moment, throwing in chaos all the Pattern right before the LB. Now he's given the orders to kill Mat and Perrin, but so far it doesn't work. The Shadow is gonna end in big trouble if it keeps not working, and it can't eliminate people like Egwene either. A very tight web is emerging through all the chaos, as if the Wheel had taken advantage of the apparent chaos to hide its plans until the end.