I tend to agree with Rosh that having the use of a weapon build its utility breaks the paradigm for RPGs where you "Learn by not doing"; such as in D&D where if you want to learn to use a weapon better you select the feat that lets you use it; and in Fallout where you put skill points into its skill.
Why not impliment Perks to do much the same thing; but instead of adding to the weapon they add to the character; for example someone with over 100% in small guns could get the following:
PERK:
Shotgun Surgeon
You have mastered the use of the scattergun as a weapon. You deal extra damage with a shotgun; move one step up the critical hit table when using shotguns, and any critical to a limb automatically criples it. You also use special shotgun ammo that would normally incur a penalty without said penalty.
PERK:
Trick Shot
You have become an especially skilled pistol user. Your pistols never jam; you can shoot them faster, and you can weild a light or medium pistol in each hand at a reduced penalty and reload magazine fed pistols thus weilded as normally. Your knowledge of handgun behavior allows you to makeke a shot beyond a pistol's normal range, as well.
PERK:
Rifleman
You are lord of all things rifle. You know just where to shoot, dealing extra damage and moving one step up the critical table. A critical to the head or eyes will always kill a man. Your semiautomatic, repeating, or single-shot rifles will never jam and your automatic rifles will do so with greatly reduced frequency. You make faster bayonette attacks and never break your weapon when striking with the buttstock. You can make an effective shot beyond your weapon's normal range.
PERK:
My Strength
(In Hebrew: Uzi)
To master the machine pistol is difficult indeed, but the rewards are great. With this perk in place you can fire a burst with more accuracy, weild and reload an SMG in each hand (Excepting rifle-scale weapons like a Thompson or PPSh, etc) at reduced penalty, and any such weapons in your skilled hands will jam with much less frequency. You can also reliable squeeze off single shots from auto-only SMGs like the Grease Gun and PPS-43.