I have taken over several planets and have stopped getting any interesting missions from the Rebels. The last one was the Alien battle cruiser. Is my ruling the planets blocking new missions? Or is that it for missions?-Drew


Nope, the Alien missions are the last for the two governments; after that, its just repeat missions, like deliver munitions, etc etc.
You might want to check out EV Game Expander; it does a great job of expanding the original EV universe (hence the name)