Sure it does. It makes characters more unique. The weapon groups system is a boon to mages, since they get such a poor selection of weapons; monks, also, can break out of the stereotype (martial arts uses a wide variety of weapons) and customize their weapon selection. Rogues get Short Blades, Thrown Weapons, and Bows or Crossbows (pretty much what they have now), bards have Short Blades, Thrown Weapons, and one of the player's choice.
I think the question of using a weapon or a different weapon is not that big of a deal. It is style and flavor choice and limiting them to "only" that flavor choice is via groups is a bit heavy handed. At least that is my view these days.
What does proficiency do? It removes the penalty to hit that is inborn with all weapons.
I think what I am going to do is the following:
Break the weapons into four groups groups again but in a different way:
Natural Weapons (Improved unarmed strike gives access here)
Basic weapons (all classes and characters can use basic weapons [club, dagger, dart, staff, sickle, and sling], druid would add a couple of weapons on top)
Simple Weapons (weapons that are on the simple list plus the added exotic weapons, rogue and bard would add a couple of martial weapons on top)
Martial (all the martial weapons plus the exotic weapons I noted)
Natural weapons: Monsters and possibly Monk
Basic weapons: all
Simple weapons: all but Wizard and Druid
Martial weapon: Barbarian, Fighter, Paladin, Ranger, and possibly Monk
So three feats:
Improved unarmed strike (for creatures without monster hit dice)
Simple weapons (for wizards and druids and monsters)
Martial weapons (for everyone but the Barbarian, Fighter, Paladin, Ranger, and possibly Monk)
Again the idea is to remove the penalty to weapons easier. If you have martial weapon proficiency and find a bad ass magical warhammer but in the weapon group system didn't have warhammer the system limited the hammer from game. I don't want to do that. Also, WF and feats like that already add a bonus for specializing in a weapon. I don't want to add a penalty to further distinguish differentiation.