I've been reading some articles recently about the benefits of making all weapon damage equal. While I do think it is a good idea I also believe it misses the point. It is a good rule that fixes many min-maxing without requiring a complete rewrite of the combat rules, but it fails to address the underlying problem. In D&D and d20 in general there is no hard rule that punishes big weapon use or more concretely that benefits smaller weapons.
Enter fatigue. Fatigue represents the second to second wear the characters suffer during combat. On a fixed attack per round system like D&D agility and fatigue play no role. Ok yes, there are some adjustments for initiative and what not, but when Joe Fighter can swing his two handed all day long at three attacks per round there is no counter force to min-maxing on weapons and on armor.
Now if we make the number of attacks per round depend on the level of fatigue a character has, armor and weapon selection come into play on a different level. Suddenly the unencumbered swordsman can wear out and the kill the heavily armored knight.
The rule can be expanded to encompass magic users and limit super powerful spell from being chain casted. Dragon breath is limited due to fatigue as well and undead become more fearsome as they never seem to tire.