Sometimes developers think about what's cool and not what's fair.
Dark colors for one team can give them an advantage in dark maps. The model of your char also has an important role. It could be smaller(Usually females are slightly smaller(In humans anyways)), the animations odd(Doing a cartwheel everytime you jump), devs might even change the hitboxes(World of WarCraft CowZ vs MunchkinZ)... Depending on your race/sex, you might even have different game sounds. It's not fair if you make louder running sounds, scream in pain, etc.
Abilities/Classes/Whatever also throw balance off, but that's usually to be expected.
// Curtis Turner - IceIYIaN
// Creator of Elements of War!
// http://www.ElementsofWar.net/
// http://www.ModDB.com/Mods/Elements-of-War