Because unless the hit was equally lethal, the longsword does more. It's much easier for me to deal a grievous injury to someone with a longsword than with a dagger (as long as I have enough space). Especially when you start counting in thick hides and the like, which could basically make my dagger worthless, while a longsword would still be somewhat useful.
I can't agree with that. A weapon is a tool for the job, and if a weapon was widely used, it is because the weapon did more damage in a particular situation. Many knights for example, carried a dagger in addition to their longsword. They did so, because once you had someone down, you could use your dagger (if you didn't feel like ransoming him) to stab him in the gaps of the armour. In the visor, the armpit, the groin etc. A clear situation where skilled use of a dagger leads to more damage than a sword.
Also, if you were carring a dagger in the middle ages as a weapon of self defense, you can inflict extremely grevious wounds if combined with grapples and holds. If you were faced with a swordsman and were skilled enough to get past his guard, a good place to thrust your dagger is the nice soft place between the neck and the collarbone. Certainly that would do just as much damage as any sword blow.
As for thick hides, you'd want a thrusting weapon to break through that. You get better penetrating power from concentrating power unto one location, not by slashing with a long sword. A dagger or a short sword is the tool for that job.
Up to this point then, the weapons are just dealing "fate, luck, skill" damage, then? Okay, seems reasonable enough to have them be the same-ish until the actual physical damage is dealt.
Well, this is designed to take into account parries, evasions and such. So minor monsters would have 1 "body blow" point so they can be one shot kills (minions or 1 HD monsters). Monsters you expect to trade blows with in a cinematic duel (or monsters which are extremely tough) would have more than one "body blow" point. If you take a plate armoured knight, the first few blows against him do nothing, then you might break his shield, daze him with a head blow, and then the last blow would be the mortal wound (and the only physical wound that can't be explained by recovering with rest).
This part I'm shaky on as well (and I'm not talking about the axe vs. club lethality part). Would factoring for weapon vs. armor only apply when the enemy runs out of "fate, luck, skill" hits? If you factor armor vs. weapons against all of the attacks, then are the first hits truly representing "fate, luck, skill"?
Largely I was figuring that weapon qualities (ie. 4th editions versatile, brutal, high-crit, reach etc. categories), along with weapon speed could get me to distinguish the types of weapons and their effectiveness.
The place I would like to get to is that weapons are recognized for being tools for certain tasks and compliments to certain fighting styles, rather than weapons that do more or less damage.
That's one way to look at it. Though now you have brawn only equates to accuracy and not to damage, which is something you may or may not be going for.
You are right there. It should either count for both, or I could see a case for brawn counting for damage instead of accuracy.
I think you're getting mixed results on abstraction as of this point, and may want to streamline it slightly from how it's presented thus far.
It is a very rough idea thus far, and I'm getting sidetracked with ideas about weapons which were designed for the HP system.