My Girlfriend and I have been forming an alliance as soon as possible when playing against AI... when we get to the end though, all other races wiped out we were hoping to have a shared victory. In the end she gave me most of her planets and then the game gave me the victory, but if we had split the galaxy basically in half do we REALLY have to fight each other once there are no other contenders?
Yes. There is no shared victory in Endless Space. Nor are there set teams - you can't, for example, force the AI to ally each other (or you!). Endless Space is a strict FFA.
It would be nice to have more options here. However there's a higher chance that Amplitude will apply changes to Endless Legend, its current project.