A weapon penetration system is usually designed around a game engine that has the ability to define material composition like unity so I'm not sure if this would even be plausible but I'll go over my ideas about it. This feature to the combat system would really bring a sense of realism and allow for new combat tactics.
The first part in implementing it would be to define an objects armor value. A wooden wall versus a concrete wall or a car door versus a armored door, bullet resistant armor versus advanced armor, etc. The second part would be the penetration factor on the munitions or AP value. You would then have the choice of ball, AP or explosive ammunition types along with the caliber size of the weapon or if it is ballistic vest energy etc. This type of system has a lot of moving parts and calculations and is where you will get lots of critiques how the weapons and ammunition should be weighted.
It would be a great system, but I think it would detract from the basics of the game too much but I think it would make a great mod!