I've had a similar thought about weapons and damage too. But instead of hit location/variable damage I've always had this nag about why certain weapons should naturally be more deadly than any other given weapon and thus have different damage dice.
I mean if you run a person through with a longsword or a bastard sword, why should one weapon do 1d8+X and the other do 1d10+X? They both are going to kill a person the same. One could argue that that particular instance is represented in the moment a character is reduced to 0 or less HP. But still, why should a bastardsword, or greataxe be more 'deadlier' than a longsword, rapier or even a dagger?
Thus instead of assigning each weapon a specific die type how about weapons starts at a base of d4 (or whatever... I just made that up for sake of discussion). Then through Weapon Focus type feats a character could expand the max damage of the weapons they 'train' in higher and get higher die types for weapons.