I'm just thinking that there should be some consistancy. If physical can be scaled down to armor, why should subdual rounds be able to ignore armor rating altogether? Stun damage just skips the armor rating comparison altogether so it doesn't matter whether he's wearing full riot gear or a leather jacket, only difference is the number of dice he rolls. Where if I shot him with regular ammo his armor would have the potential to downgrade that damage from physical to stun damage.

It would be like being shot with a paintball.

Why? Because game balance is important, that's why. Your houserule would be an absolute, unequivocal nerf. The only change you'd get is that nobody would be dumb enough to use a stun weapon except in a riot control sitution where you're trying to disperse unarmored people in a non-lethal way. The game is written so that none of your ammo options are pointless or no-brainers. Regular is good because it's cheap, gel is good when you don't want to kill people, stick-n-shock is a little better than gel but more expensive, ExEx is powerful but expensive and highly illegal, etc. Your house rule would be tossing gel rounds out the window. It would make an ammo type useless for no reason. Are you finding gel to be imbalanced? After the errata you shouldn't be. They're not very powerful at all, so they don't need a nerf to correct a power imbalance.

Also, unarmed combat would become pointless. Thanks to the STR/2 DV, a super burly human with str 6 does DV3 in unarmed combat. That would mean that if you were wearing any reasonable level of armor, you would probably be immune to a punch from a martial arts expert with S6. That's just not right.

You are proposing a house rule based on symmetry. That is a bad basis for a house rule. Yes, it's nice when the rules are consistent and symmetrical in every case, but game balance and having a variety of options is a lot more important. You have to consider more than just making everything nice-n-neat when making new rules that contradict the RAW, otherwise it will hurt your game.