The main problem is engineers taking up precious pathfinding resources when bouncing around factories.
There is a console command to increase the resources of pathfinding, it is called: "path_ArmyBudget" and it's set in the console. Cheating needs to be on for it to be changed (or if we make a non-UI mod).
I would suggest Ze_Pilot to change this default value from 1000 to 3000 and this will solve all lag connected to commanding units. Stuttering from network / cpu is still an issue.