Here are a few ideas of mechanisms I've been using in my modern warfare RPGs.

One is that damage does not depend on the weapon or armor as much as the body part hit. Simply put a 4d20 round that misses delivers no damage whatsoever. The same round hitting your hand will blow it right off, but it won't kill you (at least not right away). So in my games I've come to represent damage as an ammo's roll plus a location hit modifier. A round may do 3d4, but each die subtracts -2 if it hits an arm or leg, +0 if it hits torso and +2 if it hits the head. The actual hit location is derived from the hit roll and how good it is plus exposed body parts, and not a "hit location" table which might produce unexpected results like a hit on the foot while prone behind a low wall.

The other mechanism is damage soak by stamina. Creatures have a value called pain threshold which soaks (diverts) damage to stamina and away from hit points. A character may have 30 STA, 12 HP and 4 PT (pain threshold). A round that delivers 6 HP of damage first soaks 4 to STA and only does 2 to HP (very small damage compared to the total of 12). The net effect is that low damage rounds or rounds that hit arms and legs will have to deplete STA first before actual damage is done to HP. The same 6 HP round hitting the head would be modified up by 6 (+2 for each of the 3 dice). This produces a 12HP that soaks 4 to STA and leaves 8 HP of real damage (a significant amount when compared to the characters 12 HP).

Larger creatures will have higher STA and  PT values and not necessarily more HP. The ammo is always the same, but the effect of the ammo given the pain threshold buffer and point of impact does add up to a considerably lesser "damage effect" against larger creatures (or sturdier smaller ones, like a battle seasoned dwarf).