I’ve never been entirely happy with how bastard weapons were handled in 3.x. I’ve had characters use them where it was a good fit for the character concept (okay, one PC that I played, and some NPCs), but most of the time it’s grossly inefficient. If you want more damage with a one-handed weapon, take Weapon Specialization; if you want more damage overall give up the shield (or second weapon) and go straight to the two-handed weapon (greatsword, greataxe, etc.).
Weapon familiarity in 3.5 helped, but only for racial weapons. The dwarf got to use his dwarven waraxe one-handed as a martial weapon, but the human got nothing (again). Anyone else had to take the Exotic Weapon Proficiency feat to see the ability to use the weapon the same way.
Incidentally, I never liked how bastard weapon use was worded. In my campaign I early on changed bastard weapons to martial two-handed weapons, usable one-handed at a -4 penalty that was removed by taking an Exotic Weapon Proficiency-type feat. Same net effect, much clearer rules.
I think I’ve got a simpler way to handle this overall that both makes it simpler to adjudicate and more reasonable to get them into play.