This seems to be an evolving discussion and we've attempted to do our best to be as inclusive as possible while at the same time including the functional benefit of allowing male/female restrictions throughout the site. At IMLeagues we have adapted how we handle "gender" to comply with NIRSA's policy ( http://title-ix.blogspot.com/2015/01/college-rec-sports-has-new-policy-of.html ). Basically when you go to sign up we ask "I play Sports As" to avoid the term gender entirely. This allows the individual to self-identify at their own discretion, but it does require them to identify a gender that they are playing sports as so they can't switch between male/female leagues and for the purposes of CoRec leagues with min male/female requirements. Also, If you wish to go beyond this and prompt for a specific gender for reporting purposes (or add an option to choose not to identify) you can add a custom registration question and add as many options as you would like.
We can certainly look into adding the ability to remove the question entirely, the main issue there is as mentioned above that would either mean restricting those that don't identify to only playing in specific leagues (doesn't seem that inclusive to me haha) or only allowing Open leagues. Of course we're happy to listen to any suggestions on this topic as we absolutely want to be as inclusive as possible, for now what we've tried to do is follow NIRSA's lead in how balance inclusiveness with the benefits of male/female restrictions.
We're trying something new - a forums area that only admins can access!! Hopefully this will be a useful tool for connecting with other programs on the site, sharing best practices, etc. If not, feel free to tell us to get rid of it in the Feature Suggestions area :-)