Well I like some of the ideas on this thread but don't want to be toooo specific.
I prefer the parallel research idea to the queueing idea - having 2 researches and researching them in parallel instead of one after the other means you don't get the first one until slightly later, but you don't have to be around to start the second one. On the one hand, you don't have to be around. On the other hand, you get the first tech later than the second one.
As a covert ops aside, it needs a complete overhaul. Which will happen, I think.