I've decided to quit my current game over this issue.
The AI I'm at war with has a couple stacks of one-unit micro armies opposing me. I can either take one unit-army down, one a turn, OR split my army into one-unit micro-armies themselves, which while solving the time problem adds a huge micromanagement and tedium problem to replace it.
So, I think to myself, I'll just ignore these micro-armies, and press on, take the next city, right? Well, the micro-armies then move into my territory, where they are now a threat to either merge into a big army and attack a city, OR stay as micro-armies and destroy my improvements.
So now, I realize there really is no 3rd option, at this point I really have to split up a couple armies into micro-armies, to chase down his micro-armies. Utter game-killing mind-numbing, unit-chasing tedium.
So yeah, this totally needs to be done away with, there really is no strategy addition here, as some people here seem to think, just small army micromanagement hell. It has got to go!