I'm sure this has been suggested before, but what about different ammo types?
Armor piercing rounds (obviously) reduce the target's armor when figuring out how much damage an attack did.
Hollow point rounds (or fragmentation rounds, or exploding rounds, etc.) increase the target's armor when figuring out the damage formula, but do more base damage.
Then of course, for different types of ammunition, like rockets, you could have like High Explosive for the extra damage, or Sabot rockets for the armour piercing.
Not sure how it would work for plasma, as plasma already does a lot of damage and already is quite effective vs. armor. Also, some may see this as "unDoomish" but then again most, if not all, of the unique items weren't in the original Doom.
Anywho, that's just my two cents.