I think difficulty should be reflected in how well the enemy takes cover (note, I don't mean whether or not they take cover, but rather how well they do it) and in how accurate they shoot.
And I'm rather surprised that as much as games tout their interaction they don't let you physically interact with people. I mean, if you shot someones foot, they shouldn't walk on it anymore, maybe crawl to a nearby stick to use as a crutch or something. Things like this would help get rid of the "health = difficulty" problem. Rather than make it how much health they can absorb, make it more like vital organs + blood loss + pain tolerance. If you're shot in the heart, you die. Shot in the head, you die. Shot in the lungs, you've got a very short time to live/cough blood, then you die. Shot in the leg: did it hit an artery? if so, you'll bleed out faster, and can't use that leg.
Naturally, the hero's nano-suit would prevent these types of hits happening to him/her... but the others that don't have suits should have such things.
Oh, and when I said pain tolerance, I mean things like going into shock or passing out from the pain. The enemy's not dead, but incapacitated
Also, punching people should hurt them, or make them winded, etc, depending on where they're hit. Break someone's arm/leg and actually have it break...
While all this is really violent and potentially disgusting/disturbing, that's what's needed to get rid of stupid "absorbing bullet" enemies. Until things like this happen, that's all games have, is how many shots does it take to kill this person.