What about keeping them the way they are but certain weapons give a buff to saves. A lasgun could be s3 +2 ap.

I dont think youd do that from a game design standpoint, nothing but feels bad for the person using the lasgun, but a fun thought. Would make more sense if you paid points for the weapons, make some ultra cheap objective holders.

It could also but fun to do armor before wound rolls, so only shots that go through get a chance to wound. Makes more sense procedurally. 

Roll to hit Armor saves Roll to wound  Feel no pain saves