What we really need is a starcraft-like shift-righclick targeting cue. 10 marines on 10 marines is a coin flip on who wins. But if one player shift-attacks each of the enemy units in order then he wins and still owns 10 (50% damage) marines. The reason is that it takes 10 marine's shots to kill a marine. The one side fires at random, but the micro-manager's units all fire on a single target, killing it instantly. Now its 9 marines on 10. The enemies fire again, dealing some spread out damage, the micro'd units fire and kill a second unit. Repeat.
Or...we could smarten up the focus fire control node, which separates by ship type. So all your bombers will target the same thing, but your fighters, frigates, [special], starships will target something else (and all fire on the same target based on the unit's targeting preference).