I've suggested many time tying trains and convoy to base supply status. Basically, if a base doesn't receive a convoy every x-minutes, decrease the bunker status by 25% (then another, and another, to a minumum 25% status).  Doing the same to a train running to a factory/refinery, barracks affects supply for the entire zone.  Or something like that.  Damaged base supply bunkers could only rebuild if convoys arrive in a timely fashion, too.