I do think that the default auto-assist cutoff could be raised some, in addition to a "whitelist" of things to be repaired (aka, things that are ALWAYS auto-repaired, regaurdless of the auto-assist cutoff), and add hyper-critical structures like the Home Command Station and the Home Cores to that list.
Actually, both of those should go on Mantis somewhere, if they aren't already.
I also think that in general when a unit cannot do an action you are trying to tell it to do, the reason why it can't could be communicated far better than it is now. (Think AVWW, where it just spits a brief message about why you cannot do whatever it is you are trying to do into the message log, even something simple like that would be an incredible boost to UI clarity)