Konisforce's talk of a granularity arms race got me thinking... What if, beyond the simple measure of warhead strength, we had a 'warhead spread/scatter/subsubmunitions/focus' factor as well? Basically some way to allow a missile to hit multiple targets in the same location at the cost of sheer power. For anti-missile work, it would be optimal to maximize your spread in order to better handle salvos of missiles. It would be useless against an armored warship because the penetration profile of a fractional strength hit is, well, nothing, but that's the price to pay for specialization. If you want flexible AMMs that can double as a last-ditch offense in a pinch then you can design those too, they'll just lose out on the increased salvo handling ability.
For larger missiles with room to play, this opens up some fun options. You can stick to standard and apply your full wallop to a single target, or you can divvy up your still-sizable punishment to try to force the enemy out of formation.
Not sure how said extra targets would be picked, though random seems as good as any. Maybe just have some set fraction increments, 1/1 to just the target, 1/2 to the target and somebody else in the same spot, and so on. If you've got crowd control missiles loaded against a single dreadnaught, well, sucks to be you.
Now adding in fractional damage that only effectively affects missiles might seem a bit sloppy in and of itself, the options such a change would open up seem interesting.
Hm, and if you continued the damage attenuation of beam weapons down between one and zero it would be a range buff to PD as well, though not sure the effect that would have.