I think the title says it all, but just to be clear:
It would be nice if the AI could take a break from their automatic activities to obey those
lovely signal commands given by the captain. For instance, the "Man the ___ guns!" could be automatically followed by the gunner, while "Repair the ___!" could be assigned to one of the engineers.
The AI usually have a decent sense of what to do next, so these special commands shouldn't permanently override their behaviour once issued, just temporarily (10s?) give them supplementary actions.
I think this is most apt for commands from the pilot or captain (usually the same person). Having the engineers / gunners able to issue commands to AI crew as well could get messy.