I like the sound of not needing bays to launch units. It would make a race capable of doing it unique, provided it isn't too powerful. Or possibly even just increasing the number of units that bays could launch would work, though it would be less exciting.
As for facilities, I suppose you could combine the nexus with a more common facilty or something. Teleporting resources about the empire with out the need for a nexus fits the theme. Eh, Maybe.
