while I'm not sure that this is the best way to improve things, I do agree that stacking could be handled better, more dynamic or shall we say interactive in that we can influence more accurately what we want stacked and maybe how much so.
what could correspond your request would be an option in the options menu such as "always stack logistic buildings" or something along the lines. much like the option "always autoplace extractors".
for me the nicest solution would be to have them stacked, but be able to expand a stack of units and see the individual units too or remove move them away and form a new stack.
oh, and lastly: is there a stack attack option already? in the past when I ordered an attack on an enemy stack, it would only work on the first unit of the stack, then it would be autofire again. maybe this is an intended behavior and was never planned to change, but I would like a quick and easy option to have a selection of my units concentrate fire on all, say, lrfs or siege units. and smartly so, not that 50 heavy cruisers focus fire on 1 lrf. that would simple be a waste of firepower.