So from I understand the basic idea of playing 1 single faction with 2 players is that 1 player gets all the (blue) admiral heroes and the other player gets all the (yellow) general heroes. However the biggest problem I think with this is that the ground units can't move without the ships carrying them. So the general player would need to take the admiral player's units, just to move his stuff.
So I brainstormed on alternatives to mix the two players roles in their faction. 2 ideas came to mind.
Rebels or Imperials option: One player controls the military. The other player handles missions.
Imperials option: One player is in charge of finding the Rebel HQ, the other player is in charge of defending/other matters.
Anyone else have any more ideas?