I think that as much as we would wish to be beyond gender, a vast majority of the population isn't. I don't think having male/female bathroom is necessarily a bad thing.
Think of it this way, going to the restroom is for most people a moment where they feel vulnerable. You take some of your clothes off, and there is a taboo associated with it. Now no one likes to feel threatened, especially not when you already feel vulnerable.
Sure, most men wouldn't threaten women, but for the few creeps that exist, well I guess I don't see anything wrong with women (or even men) each having their restrooms.
Now, the whole controversy about transgender people using the bathroom they feel more comfortable in is just silly. The myth of the man wearing women's clothes to perv into the female's restroom is just laughable and frankly insulting towards trans people.