I'm sure this probably isn't a great idea as far as making gameplay "balanced" in terms of good vs. evil. But I think being evil should allow the player to have inherently more advantages then if you were being good.
Being good usually translates to being bound to make ethically and morally sound decisions i.e. you aren't making decisions solely on the basis of maximizing your chance of winning at any cost; you're doing it while upholding certain principles and values, whereas you have the choice of doing anything you damn well please if you're evil... because you're evil!
I can understand that good races will tend to stick together, and evil races will be more likely to just look after themselves and be more opportunistic. That seems pretty reasonable. But as far as alternate techs you can research or the different good/evil choices you have to make, I feel that the being evil should give you a better bonus for the most part.