A fan noted the lack of customizable attributes in Diablo 3, and asked if the male / female characters of the same class would have any differences. More strength for the males, more dexterity for the females, etc. Bashiok replied with more words than “no,” just out of the kindness of his heart.
We don’t want to force players to pick one or the other based on something like stats. If you choose a barbarian you’re choosing a barbarian, regardless if it’s male or female.
Separating them creates a choice at the start of the game that will have long-lasting repercussions on how your character behaves without actually knowing what those effects will be at creation. It forces the veteran player to choose one over the other for specific builds. “You can’t be the best jugger-barb unless you pick the male barbarian”, as an example. It effectively doubles the amount of classes to be balanced against each other. Assuming the differences are big enough to matter, and if not then what would be the point anyway?