Don't have two seperate, only male uniform and a only female uniform. Some schools have a male cut in pants and shorts, and a female cut in pants and shorts, which is great. But, then they don't permit the females to wear the male shorts even if they would feel more comfortable in this cut. (Along those same lines, don't make the female and male pants/shorts a different colour. Feeling more or less comfortable in a certain cut of clothing doesn't always relate to gender, so don't limit peoples options.)
Another thing, it's good if you want to include a male and female cut in shorts/pants, as typically the two sexes have different body proportions, but don't get rid of practical things on these clothes over style. For example, belt loops can be very useful/practical, and removing them from a design solely because it is the female cut makes no sense, especially when there are no other methods of tightening the waist.
Also, dresses and skirts can be a very good part of a uniform, as they also allow for gender expression. Just don't limit people. Have these as an option for everybody, if it's part of a uniform, anyone should be able to wear it.
Basically, just give people options. Design the uniform so students can choose to wear the items they feel most comfortable in.
(Also something to consider, dress design. Lots of people I know who chose to wear a dress struggle with it flying up/too short when the sit down. I'm not sure if there's much/anything to help with this, but maybe keep that in mind. The other thing is, a skort option in addition to dress and shorts may be appreciated, people may not feel comfortable in the dress, but not everyone wants to wear school shorts.)