Cepheus Engine has a neat little combat section. Like the rest of the game it's just begging you to modify it and make it your own (there's even a modifiable version in Word included.) For combat I can think of several options right off the bat.
In Classic Traveller combat damage was a set dice roll. Penetration vs. Armor was handled with hit modifiers. I have justified this system (http://twilightgm.blogspot.com/2014/08/combat-in-matrix.html) before. Basically armor that will stop a given bullet will do it very consistently while calibers that are too much for a given armor will blow through it fairly consistently. Damage to most bullets is capped by the size of the human body and how much meat you have to mess up. Bullets cap (pun intended) at 3D6 or 4D6 for shotguns and flak. Damage to people in this case depends on the bullet hitting a weaker area of the armor (luck with that).
The system can be justified as much as most RPG mechanics. Where it went south was with the implementation. Roll damage and subtract armor is mad easy. Lookng up mods for range and weapon vs. armor is not quite so easy.
I'd like to introduce armor as a modifier to hit rolls in the Open 2D6 system. But I want to streamline it. We already have damages and armor protection stats so let's use them. Take the armor protection of your target (say that burly pirate wearing cloth). Divide the armor protection by the number of dice of damage your weapon does (say a rifle doing 3D6). You get a -3 to hit. The negative modifiers to hit could cap at '6' or higher as you wish to preserve the superiority of armor, or capped lower at -4 or -5 to make combat more lethal. Long bursts modify the hit number only, not the dice rolled for damage.
Weapons firing many small submunitions are at a further -1 to hit armored targets. Ditto for body pistols, revolvers and auto pistols.
Weapons of a higher tech level optionally reduce the armor modifier by 1. So in the example above if the attacker was using an ACR (TL 10) vs. Cloth (TL7) the normal modifier of -3 (9/3) is reduced to -2. Blast away.
To keep lasers competitive but not on the level of phasers, they benefit from the tech level modifier. Armor of TL 8 or 9 is assumed to have reflective properties.
Next Up: More Pistol Packing