From a brief look at the damage system it seems there is large amount of damage types one for each weapon light laser , medium laser etc. which are located on the page
http://ufoai.ninex.info/wiki/index.php/Armour_table. I suggest adopting a different mechanism similar to the ones employed in some table top games. Each weapon has an armour piercing value added to it alongside its damage reflecting the ability of the weapon to penetrate armour. This would have no effect on opponents with no armour . It would only reduce the armour protection value before the damage calculation is carried out.
For example lets say weapon with damage 30 armour piercing 10 is fired against an alien with armour protection 20.
Now normally this would result in 30 - 20 = 10 damage but with the the new system it it would be 30-(20-10) = 20 damage. If the armour piercing value exceeds the armour value then it is equivalent as if there is no armour at all. Consider the example above if armour piercing was equal to 30 then the damage done would be 30 it cannot exceed the regular damage just nullify the effect of armour.
You might ask what is the point in doing this ? It means that rather then having a table 19 or 20 damage protection values you could simply have table with about 5 damage types with the fine tuning between weapons achieved with a combination between damage and armour piercing with say heavy weapon variants having more of both. This would allow the display of armour values on a small table or user interface for ease of use and reference in game.
Another possible use of this feature is using the armour piercing factor in determining which and how many walls a projectile travels through.
