I like Odysseus' idea of changing the MW price for the various classes of weapons. Not sure how the numbers work out, but it's a good thought. Of course, after a few levels, when cash isnt much of a problem, it probably doesn't matter anymore.
The simple weapons primary function for the PC classes is for those semi-martial classes like the Cleric, or the Sorcerer. Someone who needs to be able to defend himself, but isnt generally going to rely on it. Because of that, it isnt neccissary that they cary a weapon capeable of dealing 2d6 damage or a d12 with a x3 crit. These characters will often instead carry a crossbow, which as has been mentioned by several, is already on par with the average martial weapon. A class like Ranger or Fighter, while they can easily use the simple weapons, will often opt for a better weapon, something that not only deals damage, but is a mark of his character, and is just a little more menacing than the average simple weapon.
In terms of mechanics, there is of course the standard list of Weapon Focus and the like, but also look at the Style feats from Complete Warrior. They all depend on a specific weapon, or set of weapons to be used, some with the lowly simple weapon. You could even create your own similar feats, but do notice that each Style feat has a reasonable amount of prerequsites before it can be taken.
Any choice made comes with consequenses good and bad. The player knows this, he can weigh the benifits against the penalties.