[quote name='pete5883']I assume bosses never get knocked down,[/quote]The knockdown is only on killing blows. Neither the killing blows of the Mk. II nor the Mk. III matter for bosses. Knocking down, killing enemies in the crowd... irrelevant.
EDIT: I don't think the prototype's stun works, either.
[quote name='pete5883']and you're only going to get a fixed number of hits in against them before they start blocking, (so it doesn't matter how fast you make those hits,)[/quote] Actually, I was never clear on whether it was a window-of-opportunity thing or purely a hit-based thing or if it varied from weapon to weapon. I haven't been paying enough attention to that.
[quote name='pete5883']so how would doing less damage, faster, help?[/quote]Knocking enemies out of charges, not pushing them away, never having to recharge your battery (particularly dangerous when the camera decides to point away from the enemy), etc.