I agree with Sid Meier that the strategic layer make MP difficult. So why not just do MP without the strategic layer? I think you could have a really fun MP mode with just the tactical battles. After all, it seems to me that engaging your friends in tactical battles is what players really want to focus on anyway. First, there would be a set up screen, where two players would agree to their starting energy, wonders etc... Then, players would get a fixed time (say 5 minutes) to use their energy to customize their fleet) and then when the timer is up, the tactical battle begins.