In the Simulacrum, options to add red doppel/ship spawners and stunners are available. Could the blue versions of these be added as options as well? Since the blue doppels/ships need some sort of path to follow, they could be programmed to head towards the nearest enemy emitter/doppel/ship/structure. The Simulacrum menu might need to be expanded to fit the new options.
Those options and a few others (Omni Limits as an example) should definitely be a part of the Simulacrum. I don't know how, but I can dream.