I've spent the last few days trying to balance out something based on some suggestions here. See what you think; it's based heavily on the 2E system. Kinda long.
All weapons are divided into 10 basic groups. Let's think of them as:
Slashing (swords)
Chopping (axes)
Polearm (spears and polearms)
Blunt (maces and hammers)
Piercing (daggers)
Projectile (bows and crossbows)
Thrown (darts and javelins, plus you use this proficiency when throwing any spear or dagger)
Flexible (flails, nets, and whips)
Natural (unarmed attacks, gauntlets, natural weapons, touch attacks)
Rays (ranged touch attacks or firearms, anything point-and-shoot)
Then, split the groups based on the PHB weapon size, into Light (smaller than your size), Medium (your size), or Heavy (one size larger). That is, Longswords are Medium Slashing, Greatswords are Heavy Slashing. Obviously, this varies with the size of the wielder; to an Ogre a Greatsword is a Medium Slashing weapon. (Special case: double weapons go as each end, so a double-bladed sword is Medium Slashing instead of Heavy, like two longswords; a quarterstaff is two light maces, and so on.)
Rays and Natural only have one possible size, Light.
When you gain a proficiency (with a Feat or by taking a class), you gain all three sizes, so it's one Feat to gain all Slashing weapons. Likewise, each class starts with a couple specific proficiencies, immediately picks 1 or 2 more, then gets a couple more as they progress.
So, Rangers might automatically get Projectile, plus 2 of their choice quickly and then a few more later. Paladins might start with Slashing and Blunt, and add one every four levels. Monks get Thrown and Natural. Fighters pick any 4 and gain another one every two levels until they have them all. The key is to spread them out over a few levels so that multiclassers don't get them all right away.
Clerics get the subgroup (group AND size) that contains their deity's favored weapon. All caster-types get Ray. And so on.
(Druids get a couple groups too, with the limitation that using nonorganic things add an Arcane Failure-type penalty, similar to Monks)
But, when you take Weapon Focus/Weapon Specialization/Improved Critical/etc., they're only for one size of one group, and apply to all weapons in that subgroup. So, Weapon Focus: Medium Slashing will help with Longswords, Scimitars, Two-Bladed Swords, Gythkas, Wakizashis, etc., but not Greatswords (Heavy) or Kukris (Light). That gives 26 possible groups to put those Feats on.
Also, IMC every character automatically is proficient with all Light weapons (that's every weapon below your size), whether they picked that group or not. Frankly, it never made sense that certain weapons, like a small hammer, required that much special training. This mimics the Simple Proficiency rules, since that's what most of those weapons are: across the board, light weapons.
Exotic weapons are a special case. Each has two (or more) proficiencies. One is normal, and carries the usual -4 nonproficiency penalty. The rest are Exotic groups, each of which gives a certain benefit, and each Exotic Group requires an EWP. If you don't have that EWP you can still use the weapon, you just don't gain the benefit..
For example, the Double Weapon group is easy: without taking Exotic Proficiency (Double Weapons), you can't use it as a double weapon. You can still use it as a single weapon, using the stats of one end.
Other exotic groups: Monk Weapons (unarmed attack progression), Heavy Weapons (Bastard Sword and such), etc. Some classes get specific ones for free, like Monks getting (duh) Monk Weapons.
You can also bring races into this. Elves get the Projectile group for free, plus either Slashing (medium only) or Piercing (medium only) for the longsword/rapier thing. Half-Ogres get the Heavy Weapon exotic free. Gith get the Flowing Weapon exotic for free.
The nice part is, this means every weapon falls into one of only 10 mundane categories, plus 7 exotic categories that overlap. This makes it really easy to add new weapons to the game as treasure, since you don't get the "nah, I've got Weapon Specialization in longsword, I wouldn't use that" syndrome.
I'm still trying to balance out number of groups to give each class, though.