Civ4 did this pretty well. There were some clearly unbalanced trait combos, but this wasn't a problem for game balance as you could only access them via the custom civs.
How do you figure? In BtS pretty well every trait combination is available on some standard leader.
But not all. And the ones that are missing, Ind/Phil in particular are probably unbalanced.
Also, the trait combinations where more unbalanced in the vanilla game. Overtime they were tweaked, and evened out. I would imagine a similar strategy would work with Elemental. Concentrate on game balance/AI development for the preset/fluff races. As remember, the AI has to be taught how to play to the different strengths and weaknesses of the different factions.
As the game is polished, more love and attention can be given to the custom factions. And no doubt the community will create some anyway. But getting the basic races working (including AI) should be the priority.