I figured the homebrew board would be a good place to ask this question:
Why can't a monk use any weapon he pleases with flurry? Are there any balance reasons? If I allowed a PC in my game to do this, what would be the ramifications?
Monks can currently use monkweapons, like the kama. A kama can be enchanted & buffed all sorts of different ways and still used in a flurry. So if my PC wanted to use a rapier instead, would that upset things?
I'm tempted to say that only one attack per paired BAB can be used with the rapier, the other attack must be unarmed (slash! kick!) Is this worth spending a feat on (making a rapier monkish) or is it fine enough to just houserule in?
Eberron has Double Steel Strike, Serpent Strike and Whirling Steel Strike. You could use them as a base for designing feats that allow other weapons to be used with Flurry.