Well think, you are trained in a weapon that is very similar to another. For example, if you know how to fight well and have Weapon Focus, Improved Critical, and various other feats with a rapier, wouldn't a similar weapon per say an Elven Thinblade be allowed for you to apply to those feats?
And what if your weapon breaks? Yeah they are masterwork, but so is your opponents weapon as well, and they have a weapon like a Greatsword and you have Bastard Sword. In effect if you wield a Bastard Sword in two-hands it is like a Greatsword so why not allow the feats you have put into that weapon be applied to that one. Even bows are very similar as well.
All I am saying is that it is nice to not be screwed over due to specializing in one weapon. And it makes weapon feats more appealing, at least to me that is.