How about just getting rid of the silly mechanic and adding some "anti-focus" factors that mimic the real world, such as damage and/or accuracy that scales with range to the target and a reduction of combat effectiveness (rate of fire and/or accuracy decrease) for damaged ships?
I agree. The reason focus fire is so important is because a ship at 1 HP is still just as effective as one at full HP. And even moreso, a ship at 1 HP can be repaired!
10 ships vs 10 other ships. One fleet micros, the other does not. The microed fleet focuses fire and kites any that get too damaged. As a result, the non-microed fleet looses some ships while the microed fleet does not, which further tips the scale of the battle into the microed player.
First things first, shields encourage focus fire. Why fire on 100 targets that are all charging their shields when I could focus fire on 10 targets and negate that advantage for 90% of the enemy's forces? Second of all, low projectile speed and useless husks discourage focus fire. If a ship becomes disabled at 25% hull (but doesn't blow up), and if firing takes a couple of seconds to reach the target, the person focusing fire will waste a few seconds of shooting as the target is already down and furthermore, even when destroyed there is still ammo in the air.
Increased accuracy for lower range would also help. If everyone is focusing fire on my capital ship and it falls back, luring everything closer to the rest of my fleet, that other fleet should take even more punishment.
If I ever get off my bum, I'll develop a stack attack mechanic for Civilization 4, and from there a fleet mechanic for the space mod in it. And ships will loose effectiveness as they take damage.