While you might be able to use math as a base for balancing your factions, I don't think it would really be all that effective. You wouldn't be able to take into account what units work well with others, like the combination of the Ornithopter and the Battle Machine, or lots of other things. Warlords 2 lets you pick which units to include in your faction during custom games and it works quite well, but that's a much simpler game where units have about three statistics each and combat strategy simply amounts to which units you put up front and which ones you put in the back, so whether you have a minotaur or a treant really doesn't make that much of a difference. In Glest, you have to take into account HP, EP, attack strength, attack speed, attack type, movement speed, sight radius, cost, production speed, armor strength, armor type --the list goes on-- and all of these things can interact in unexpected combinations.
Long story short: I think the only way to balance your factions is to test them against each other.
