Weapon lists come from wargames, where they make sense completely. Your untrained peasants armed with farm tools are probably not going to do well against my untrained peasants with halberds and crossbows. When D&D came along, these lists made for a convenient way to differentiate classes in combat. Clerics are restricted from using sharp weapons in old editions, not because of some holy oath, but because no blunt weapons do as much damage as a two-handed sword.
In D&D, I like the ability to deal damage to be tied more closely to training and experience than to either choice of weapon or inborn advantage. It matches what I’ve learned in both the martial arts and the military a lot more closely that way; knowing where and how to strike an opponent is more important than brute strength or even what you're armed with. A lot of the people I play with have at least some martial arts experience too, so house-ruling the combat to work more realistically removes a layer of abstraction that doesn’t add anything to the game for any of us.
uhhh nipple...?
1. There’s no good reason my wizard can’t use a sword to kill people.
2. There’s also no reason he could do more damage with it than your fighter can with a dagger, because your fighter should be better at finding, say, my spleen.
My answer is class based damage. Fighters do 1d8 damage regardless of what weapon they’re using, thieves do 1d6, mages do 1d4. This also applies to unarmed combat and improvised weapons, because it is both A) realistic and more importantly B) awesome if your first level fighter is able to throat punch a man to death or take him out with a ladder.
Jackie Chan would've been too obvious. Photo by Laura Johnson.
I started to look for an image for that but decided against it. You're welcome.
Yes I know that none of this addresses the point of the “weapon lists are a bug” rant in any way. That’s because role playing is an extremely subjective term and coming up with a universal definition seems not only really really difficult but also without much benefit.