Surely the sensible and 'gender-neutral' thing to do is to let all students choose between skirts, trousers or shorts in uniform colour. Accommodate a variety of preferences and body shapes while still keeping the idea of a uniform. Short skirts aren't any more of a problem than too-tight trousers. If some people are breaking the rules, the solution isn't to remove choice for everyone.
I had to wear an ugly tartan skirt as part of my uniform. Of course I didn't like it at all. I'd have hated trousers more, because I had a tiny waist and very large hips/bum/thighs from age 12. As a teenager I was horribly self-conscious about it. Standard sized trousers do not fit me at all. I'd definitely have picked the ugly skirt, no matter how disliked, over uniform trousers if there had been a choice. As an adult I can buy flattering skirts and dresses and actively avoid workplaces which would require me to wear ill-fitting trousers.
Some people, I know, feel the opposite way to me and would choose trousers over a skirt every time. Why shouldn't uniform policies allow a reasonable amount of choice?