actually i kind of like them for the flavor alone. galaxy feels more alive if there are some lesser powers screwing around but not really competing for victory. gameplay wise, they don't really serve much of a purpose and open some abusive strategies. i guess that's why they are set to "none" in the default settings?
they could probably add some features to integrate them more in the game. for example, a mid-late diplo technology that allows you to absorb minors peacfully through diplomacy (a la star trek "federation").