by lomn
As above, I think assigning each team the status of "player" with respect to the game's rules is your best bet.That is, if you have players 1 - 6, and players 1 and 2 are Team A, then A's wins (never just 1's or 2's) are used to determine starting Stars vs Missiles, pack openings, naming the world, etc. 1 and 2 can fight amongst themselves if their team gets to name the world, but other than that, I'd suggest letting the active player make the decision (for end-of-game rewards and the like).
Alternately, you can play without teams and with the understanding that not every player will be in every game. The game will work just fine that way.