Having different guns fall under agility, dexterity, and strength feels really weird. It's a completely artifial distinction, and also locks you into the weapon combinations.
Maybe instead of that have things like "aiming," "eyesight," "steady hands," and "quick reactions"? So heaving a rocket launcher would need a certain Strength (+steady hands), low levels of which would subtract from the aiming skill (Dexterity), etc. And "eyesight" would then be important for firing it at a longer range. And having a low explosives skill could cause the stuff to blow up in the air or in your face. Although I don't understand why a rocket launcher would be under "explosives". It's not dynamite, and you're not really setting a fuse. You're just firing it like a gun.
Sorry if the last paragraph was a bit unclear, kind of hard to create examples without an actual system.
Anyway, or we could just choose 1/2/3 weapons to benefit from our "prefered weapons" skills. And then choose 2 more to benefit from "secondary weapons skills". It may make a little less sense (now that I think about it, it probably actually makes more sense) than having it be directly Str/Dex related, but it will help people avoid being locked in to stuff like Rapier/Pistol combinations.
PS: And actually, the most important skill during melee combat is neither Strength nor Dexterity, but Endurance. That, and knowing what you're doing. Experience, in other words. As the masters say, strength and speed are fasle gods. I demand being able to exhaust my enemies!
PPS: This is getting to the point of being silly, but it would also be cool to be able to invest points in reserves of fat. Being fat is good.