Oh, having two seperate teams actually goes by pretty quick from my experience. Provided the players adequetly participate, the flow will go off pretty well for both groups.
I wouldn't mind a little slower; I woudl advise not to wait for the other team if that makes any sense. In my other game, we currently have two teams, neither of whom are ever on the same plane of time. Why, we have a week off between this mission and our next, which will put us a total of 9 days ahead of the other group if we skip ahead entirely.
I wouldnt' mind two groups; it's better than all thsoe characters going to waste, and with my own games and my own university, there's only so fast i can be anyway. Plus with my timezone difference to at least a few of the players, I probably won't even notice the difference