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.
Bastard weapons are all treated as two-handed as a base. Most are martial weapons, but spears (the ones between ‘short spear’ and ‘long spear’) are simple weapons. They may be used one-handed at a -4 penalty. If you have Strength 15+ you may use them one-handed without penalty, and you may do so if you have specific training (the equivalent of an Exotic Weapon Proficiency feat for the martial ones, or Martial Weapon Proficiency for the spear (feat or class ability).
This strikes me as a pretty decent balance. If you’re strong enough, you get +1 to your damage over the normal weapon (d10 for bastard sword vs. d8 for a long sword) without tying up a feat to pay for it. It’s free, but not worth as much as Weapon Specialization, and the Str 15+ minimum means you’re trading off at least +1 from two-handed use for the benefit.
This means that for Str 15-17 you do the same damage one-handed as two-handed (barring Power Attack) and leave the other hand free for other purposes (shield use, Two-Weapon Fighting, and so on. At higher Strength and/or with Power Attack it’s probably worth going back to two-handed use (so you’re likely to go straight to a two-handed weapon… unless you like the flexibility of choosing as you go).
This gives a simple rule for allowing the use of bastard weapons and justifies their use mechanically. It certainly suits some builds, but it’s not so broad that all characters would gravitate to them.