Yes, the ultimate question on proficiences to reach basic competence is, if the fighter needs those for each weapon or weapon group, why does the magic user not need them for each spell or spell group?
Or if you want to go all the way back, why does the magic user get to learn a set of spells based on his Int, and can grow this list organically in play, while the fighter can't do likewise? If you wanted to model basic proficiency in a way that keeps the peasant from picking up the sword, but actually simulates how "basic training" in a weapon might take place, you could do worse than make some fighter weapon analog of the 1E magic user spells knowns mechanic. So eventually, any fighter with a decent Int is going to get proficient in most weapons, and the higher Int fighters have got a better shot at getting proficient in the ones that matter to them. (Better grant a few free picks to start, like the free magic user spells.

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Really, basic proficiency in a weapon isn't that hard to learn--especially if you already have built up the muscles involved, some stamina, and know a bit about grips and footwork. It can't be any harder than learning a new spell. (For weapon, make it an Int roll, but give martial characters a bonus, lousy weapon users like wizards a minus, and the cleric/rogue types can cope at base.)
As an extension of this, it might be interesting to require proficiencies in all equipment--including magic equipment. Suddenly, that's why that +1 sword is nice--it works just like a regular sword for proficiency purposes. But find a flaming longsword (of any plus or none), and you'll have to get proficient in it to keep from given yourself some singed eyebrows.
