Consider two fighters of equal hitpoints, one armed with a dagger and the other with a long sword. It seems obvious to me that the one with the sword has an advantage over the fighter armed only with the dagger, but how to model this? By changing the dice used as damage of course.I have no objection to his preference for using different damage dice, in contrast to my preference not to. What I can't agree with is the "of course". First of all, the trivial objection: even if you decide a sword should do more damage than a dagger, that doesn't mean you have to change the dice used. The Fantasy Trip (Melee) didn't; it used nothing but 1 or 2 d6s plus or minus a modifier. Some old-schoolers use a simple three-damage system: roll 1d6 for average-sized weapons, roll 2d6 for others -- if the weapon is small, drop the highest roll, and if the weapon is large, drop the lowest. Changing swords to d8 for damage instead of d6, or lowering daggers to d4, seems "natural" to certain people because that's the system they're accustomed to.
Second, for this specific example, a dagger can kill you just as dead as a long sword. The advantage isn't "damage output", it's the length of the weapon. A swordsman can keep an opponent with a shorter weapon at bay while still doing damage. I prefer to handle the differences between weapon lengths by allowing characters to maneuver into or out of reach.
Third, as I've said before, different weapon damage systems have different advantages and disadvantages. I don't like the disadvantages of systems where each weapon does a different range of damage, but I like the advantages of a single d6 damage system. I never, ever have to look up how much damage a weapon does. I never worry about how much damage a new made-up weapon should do. I never worry about players all choosing the the same weapons because they're the "best" weapons in terms of damage.
So yes, I appreciate that some people who read my blog don't agree with having all weapons do 1d6 damage. I understand your reasons for disagreeing. I respect your decision to use the system you prefer, just as much as I prefer the system I'd rather use.