I realize this is a very old thread, but I just wanted to say that I had this issue today with a friend playing a dual weapon dwarf. He wants to use a dwarven waraxe MH and handaxe OH for the light weapon. In the Ultimate Combat book, they have a table of weapon categories (axes, swords, etc.). I made a GM decision to let him take axes so that he doesn't have to use two feats so that he can use his OH weapon effectively.
Paizo seems to do a great job of using common sense in their rules set, while keeping things balanced (like the ease of getting whirlwind attack). I think that this approach fits in with their general thinking and makes sense to me. I understand that the feel of a short sword as a piercing weapon and a longsword, as a slashing weapon, is going to be much different. The GM should make the call and do it before the game starts and lay down the rule to everyone for clarity.
Anyone else done this?