What's stupid is that there are weapons that need a backup, or you will struggle if you try to use them on their own.  That's just bad design.  All mission have some armored enemies,  even if not invincible ones.

I have noticed an ancient power armor enchant that gives a chance of attacks becoming armor piercing, but anyway you shouldn't need that to make weapons functional, and it's based on deflect so not as good for ranged. 

back up weapon is a stupid idea since it add unstable and not nessecary invest of a build.

but the ability, perk,echant, such thing to grant a armor penetration or break passively,

is what really should be done

Maybe you should make sure every weapon has an armor skill,  then people wouldn't run into this situation.  Maybe some people might want to use one particular weapon they like, but have to have something else as backup to deal with armored enemies. 

Even better would be the ability to edit weapon skills similar to psyker skills.