I agree that it seems odd not to include a Versatile-type damage bonus for all two-handed weapons, but I think that can be rationalized by the (usually) larger damage dice listed for two-handed weapons. This way, it's really only the greatsword that looks out of place.
Without an explicit rationale from WotC, I'm inclined to think that giving the greatsword 1d10 damage was a typo, and that it should have been 1d12 all along. Applying this "house-errata" should take care of the weapon-balance issue -- greatswords are once again worth using in their own right, and bastard swords still have enough appeal to make them worth a feat.