I think one of the only ways to solve this problem with logistics would be for a team of two to be able to control ANY unit, fleet, planet, etc. on his own side. You could have different colors for each player (just to differentiate who built what ships and took which planets, as well as to see which units they control in combat). Otherwise, it would be impossible to launch a simultaneous attack on an enemy planet unless both teammates moved their fleets at EXACTLY the same time, otherwise you have two planets going.
So in summary:
Galactic map: can move any ship on your own side, can only build things on planets your units take over (side with the most ground units left gets planet if attacked jointly, the other side's get put in space).
Oh, and I think it would be fun to have to watch every battle even though you arent a part of it, that way every player's screens switch/load at the same time. Plus, since you will be able to move around your allies ships, chances are you will ahve a fleet that consists of both your units, thus both are taking part in combat.