In TA, you would assign factories to groups, and any unit produced would then automatically join the group. Also, the rally functionality was much expanded, you could queue up standard unit commands for the factory, and any new unit produced would then execute them. If I remember right, hitting the group key would select the group units, but not the factories. Keith will correct me if I got that wrong, I haven't played TA in a long time.
I see where that could be really easy way to get factories exporting ships in a specific group. But if those ships are then on the wrong planet, I'm not sure the value of having them in the group. In the AoE series, I used to make a habit of placing key barracks and stables in control groups so that I could quickly get back to them specifically (rather than the units they produced). However, that was usually because I needed to refill their queues, but in AI War, TA, and SupCom of course that is unneeded what with the looping queues and all.
I guess this is one that I could see going either way, the AoE way or the TA way. But, given that the game plays more like TA than AoE, in my opinion the TA approach wins out here -- you guys have convinced me. I've added this to my todo list (to be done like netWilk describes above), so if anybody doesn't like this change speak now or forever hold your peace.