Agreed. By removing encumbrance, SD had removed one of the main equipment balances in the game. To offset this, weapons especially need to be associated with their new equipment balance mechanic: proficiencies.
Yes, i think that the Pathfinder roleplaying game is a very good example of weapon and armor proficiencies:
Light Weapons: Bow, Dagger, Staff and Sword
Heavy Weapons: Axe, Crossbow, Maul and Spear (-3 initiative)
Leather Armor
Chain Mail (-3 initiative)
Plate Mail (-3 initiative)
Leather Armor: -1 initiative and -10 dodge for a full set
Chain Mail: -3 initiative and -20 dodge for a full set
Plate Mail: -5 initiative and -30 dodge for a full set
All proficiencies are in the general tree
Assassin: Automatically gets Light Weapons and Leather Armor
Commander: Automatically gets Heavy Weapons and Chain Mail
Defender: Automatically gets Heavy Weapons and Plate Mail
Mage: Automatically gets Light Weapons and Leather Armor
Warrior: Automatically gets Heavy Weapons and Chain Mail