I'm a rather accommodating person, but don't worry, if it REALLY bugs me, I will speak up and disagree :P If I can work with something, I'd mostly seek out tweaks or if the thing is open enough, the chinks can be worked out during the play itself :P

Hnnnnnnnnnnnnn. . . . . I have a few ideas to cover the spectrums of kinds of creatures. Let's see if I can list the idears :P

Natural Sleep Patterns(Vampires, Owls, Felines, Fairies, ect)
Disposition(Weres, Elves, Dragons, ect)
Worship(Dwargies, Striders, Beastmen, ect)
Intelligence(Owlbears, Demons, Displacer Beasts, ect)
History(This last one is for those that made the decision on sides so far back in time, the side they are on is as natural as breathing)
And for our own personal creations, we can come up with why they are on the side they are on. 

These are all I can think of off the top of my head, feel free to drop in your own ideas on why they are separate :P