If we have these in the future, I think it would probably be best to appoint two random elemental masters (probably opposites or "rivals") as team captains, then let them choose which elements they want on their side. That's about as fair as we could get on a consistent basis, and if it's in any way unfair, we'll just have the elemental master to blame for picking poorly.
In fact, there is nothing stopping anyone from picking teams now. This would be for future reference, not for the evil vs good competition if it ever happens. So if yall think it's a decent idea and worth your time (either because it's a good idea or you're just curious what kind of team you'll end up with), please contact the elemental master of your "opposing" element (found on the metamorphosis page), figure out who will pick first, and go at it. An alternative picking method of picking one element at a time, would be the person that picks first gets on pick, then the second person gets two picks, and after that you both get two picks until there is only one left, and that element automatically goes to the person who picked first.
If yall feel like doing that, just figure out a way to randomly decide who picks first, and if you can't agree on a picking method, randomly decide that as well. Oh, and post your results here if you wouldn't mind.
Edit: Oh, one other alternative picking method would be that when you pick an element to be on your team, the opposing element automatically goes to the other team. So if light and dark are the team captains, light goes first (by random chance of course) and picks fire, then dark automatically gets water. Then dark picks aether, so light gets time. This would allow for an opposites war like SG intended, but a little more "fair." Plus, the team captains have to really think about which elements they pick, and in which order, because you want to create synergies on your side without giving your opponents synergies on their side.