Agreed about the decision, but doesn't it seem a bit cheap to you that a fighter (the expert in weapons and war) would be brilliant with a greataxe and just okay with the battle axe? Great with the heavy flail and just okay with the light flail? The second-edition fighter was good with all weapons, so you could immediately swap with whatever new weapon you found if it was better. Ultimately I think that would make the game more satisfying for the player, if he doesn't need to discard 80% of the new weapons found just on the basis that they're not the chosen type.Ugh, please don't use weapon groups. It's far smarter to have artifact weapons with some special property (such as +6 for only 5 "enchantment points" or +4d6 damage for only 4 "enchantment points") for the more obscure Martial weapons (that is, not Longsword, Greatsword, Greataxe, Halberd, and Longbow) and the exotic weapons (Bastard Sword and Dwarven Waraxe). Having to decide whether you use a better weapon that you're not quite as good with is an interesting decision.
[edited as kukri was a bad choice, see http://www.d20srd.org/srd/variant/buildingCharacters/weaponGroupFeats.htm for a more complete idea]