bases moving 2 in combat = minor problem.
using emergency propulsion to move bases. Hmm. Can you make it so that only a space yard can repair it? That way an engineering dept. cant be used to give a base unlimited movement. The player would have to use a spaceyard ship or base space yard to make it work every turn.
engineering lvl II = 1 repair and + 10% maintenence reduction. Lvl III = 2 repair + 10% maintenence reduction.
Will the maint reduc stack though? I do not know. If the wife allows I may get some time to test the theory. 
is it possible to make a component that only repairs certain other components? That would allow for successive engineering components that eventually will repair any type of component. Maybe the first repairs only engines, then engins and weapons, then engines and shields...etc...
Just more storming of my brain.
CHeers!
Trajan