This can be done by creating a trigger with a timer and effects that moves the unit to a waypoint and fires the trigger that will be the next waypoint. For each unit this can take a lot of triggers. I have an idea that will use just one trigger for all your npcs and all their waypoints.
I will describe how it works for one npc, to keep the description simple. First, place flying units as waypoints. Shrink the flying units so they are not visible. Then make a trigger with a timer, as usual.
The effects of this trigger will be 'move to unit'. The npc will move to a flying unit (waypoint), whilst that flying unit will move to the second flying unit, and so on, so the final flying unit will be moving to the npc. Loop the trigger and away you go.
The effect of this will be that the npc will move to waypoint after waypoint endlessly, just like the old system.
Of course, any amount of npcs can use this one trigger.
The irony is that a scenario will work better with the old system, since more units lag but more triggers don't. Ah well, I still think it's good.