Keeping some sort of proficiency system is important. You don't want the "Tank Mage Syndrome", because it really takes something away from the fighter-types. If a Wizard wants to use weapons, he can take a level or two of a more mundane class.
The problem with a skill-based system (like Gothmog has) is that someone usually knows by level 1 what weapon types they want to use, and don't really change from that over their career. So, while a Fighter is proficient with ALL non-exotic weapons, he doesn't really need to pay for more than one or two types. So, giving all melee classes extra skill points to compensate just ends up making them stronger in the long run.
IMC, we reworked things a little bit, making it closer to the old AD&D system without messing around with proficiency levels. The short version:
1> Every weapon falls into one of eight categories: Bladed, Hafted, Blunt, Piercing, Projectile, Thrown, Ray, or Natural. A Martial Weapon Proficiency gives you proficiency with all weapons within the category.
Fighter-type classes (and Druid, but not Bard) get one category of their choice at CHARACTER level 1. If your first level wasn't one of these, you miss out.
Most fighter-type classes also get one SPECIFIC category at class level 1. Ranger gets Projectile, Paladin gets Bladed, Rogue gets Piercing, Fighter gets Any 1, that sort of thing. If you multiclass into or out of these classes, that's pretty much all you get.
Most of these classes also get one category (of their choice) every few class levels. Fighters get one at every odd level, the other full-BAB types (Paladin, Barbarian, Ranger) get one every 5 levels, and the 3/4-BAB types (Rogue, Bard, Psychic Warrior) get one every 6 levels.
Prestige Classes do something similar.
Anyway, you could stop here if you really wanted to. If your Wizard wants to use a sword, one Feat gets you all the slashing-type bladed weapons. I include the rest of the rules for completeness:
2> When you buy Weapon Focus, Specialization, etc., you pick a category and size. So, if you wanted to be good with a longsword, you'd buy Weapon Focus (Medium Bladed), which'd also give you the bonus for similar weapons (like a scimitar), but not greatswords or axes or anything.
(Double weapons have sizes and categories based on the stats of their weapon heads, so a quarterstaff counts as two Small Blunt weapons, even though the staff itself is Large. It's just two light maces stuck together, after all.)
3> Everyone is proficient with all light weapons. This replaces the whole "Simple weapon" thing. You don't really need this rule if you don't want it. It changes things a bit; everyone can now use a shortsword, but not a heavy crossbow.
Since all Natural attacks (including unarmed attacks and gauntlets) and all non-firearm Rays are light weapons, you don't usually need to pay for those categories in step 1.
4> All Exotic weapons are in one of the 8 categories listed in step 1, but each also has at least one Exotic category: Double, Heavy, Monk, Entangling, and so on. An EWP gives a specific benefit for all weapons in the exotic category (so one Feat lets you use both ends of all double weapons, assuming you also know their Martial categories from step 1). You can use these weapons without the EWP, but you don't get whatever benefit the EWP gives. There's no nonproficiency penalty for missing an EWP, except for a couple specific cases (Mercurial weapons, for example).
For example, the Bastard Sword is a Large Bladed weapon with EWP (Heavy Weapon). That EWP says it can be wielded as if it were one size smaller. If you buy that EWP (one Feat) it also lets you use other heavy weapons, like the Dwarven Waraxe, Katana, Fullblade, Elvish Thinblade, and so on.