Why should people get a better benefit out of using a military two handed weapon than a using two hands while holding a superior weapon?
Flavor wise: A bastard sword is smaller then a greatsword so why would you get more damage out of it? Listed as in the book: Greatweapon is found under two-handed weapons, bastard sword is listed un One-handed weapons. There's a magic weapon in the Adventure's Vault that even specifically mentions that when you are wielding a weapon with two-hands as opposed to most of the "when using a Two-handed weapon" listings.
Superior does not mean "better then all military weapons." It's just better then it's military counterpart or just something speacial on it's own, like spiked chain. Bastard sword is a better long sowrd, Fullblade (which is a superior Twohanded weapon) is a better Greatsword. Execution Axe is a better Great Axe.
Bastard Sword =|= > Greatsword just beacuse it is a superior weapon.
Edit: I wouldn't having a problem house ruling that Versatile weapons count as Two-Handed weapons to small races because when they use them two-handed they do not benefit from the Versatile property.
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