Think about it for a non-MA then. The enf will sure be perking that Engi, Soldier, Doctor, etc.
This suggestion can't be balanced around %increases based upon weapon skill. You have on one hand professions with extremely solid weapon skill armor, weapon buffs, research, etc. On the other hand, you get professions who can't get their weapon, nanoskill, or evades that high by themselves. What difference is it really going to make if that Engineer gets a %boost to his pistol perks based on his sucky pistol skill that can't be self-buffed? What difference does it make to give more % healing to that doctor on his perks based upon his BM when he still won't be able to outheal damage from Enfs, and is still horribly weak to Drains and NR perked toons? Oh that's right, you just change the %
If one profession can inherently buff certain skills higher than other professions, and that certain skill contributes greatly to the effectiveness of %based perks, then the system will get so convoluted with different %s that we should just leave it as is, and increase stat values on different profession's perks.