I see people complain that they get Bastard Sword proficiency, but I'd rather have the Rogue's rapier -- you can finesse the latter.
Rapier really doesn't fit a ninja. I think the Bastard Sword profiency is largely because the Bastard Sword is analogous to a Katana, and there's lots of contention about whether there was ever a real ninja-to, or if katana would have been used.
I just can't imagine a ninja prancing around and pulling a D'Artagnan, waving around a whipcord thin needle like sword designed for dueling.
Banshee