The harvester is a bit fragile lately. So how about the commander can trigger an ability on it so it bends over and hides his fragile yellow ball inside of him. He should be lower to the ground, become a smaller target and get some sort of armor bonus against bullets and explosives. When hiding the harvester doesn't generate any res and changing in this mode requires some time to change back.
This way a good commander can protect his harvester from bulletfire from afar at the expense of not getting any res. this gives him more time to send in aliens to defend him. Off course axes, ARC's and flamethrowers always deal full damage.
This could already be usefull in alot of current maps.