Small point. "Male" and "female" are not genders. Men and women are. Animals and even plants can be male or female. It is a biological distinction as opposed to a cultural one. Animals and plants are not men and women. A transgendered woman is biologically still male.
If we are going to keep a binary paradigm in regard to facilities, perhaps they should be designated "Male" and "Female" in that they service people according to their biology and not their gender. After all these facilities are often about issues surrounding anatomy (seeing body parts that are usually not seen--in public showers or changing rooms) or in physiological activities--waste elimination. Transsexuals would use facilities matching their new anatomy. By emphasizing male and female rather than man and woman, we would learn over time not to assume that a person's use of a facility is necessarily correlated to their gender.