I don't think this will happen for a variety of reasons, some of which are valid gameplay concerns and others are... not...
Gameplay wise, riot puts extreme effort into making each champion unique looking - this includes everything from weapons to silhouette and animations. The idea is to know who you're looking at in a mere fraction of a second. Skins generally change colors, but the basic shape of a champion is still essentially the same. A skin to make champs convincingly look like their opposite gender might exceed the boundary of easily recognizable.
Take, for example, Janna. One of her current defining features is her huge mass of windswept hair. If you redesigned her as a male, presumably she would have to lose some of that since males typically (and there are exceptions, see taric) have shorter hair. Additionally, the male form is typically not as slender as Janna's model. I'm not saying have someone the size of Braum floating around, but even Ezreal or Draven, two of the skinnier male champs, aren't quite as slender as Janna is.
Now, some champs could certainly work it better than others. Draven springs to mind as one that could probably rock it. But there are some difficulties in general.
Now, another concern would be new players - who already have to learn the 140 or so champs - getting confused by a skin that alters the champion that much. I believe gender is one of those key identifiers. If I say "that tank with a hammer" you could think of Poppy OR Taric, which have very different playstyles. Altering gender might add another layer of complexity onto the new player learning curve.
The last reason is desirability. Riot makes skins to sell. I personally don't know how much demand amongst the general playerbase there is for a skin series like this. Yes, there is a very specific market for this sort of thing, but outside of that how much can riot count on for sales after the initial release? Additionally, if they made a few skins as a trial, people who want other champs will be clamoring to get their champs swapped. This would be especially bad if Riot decides not to continue the skin line, because people will have examples to point to and say "they could do it if they wanted to"
So while it sounds like a fun idea, it does open up a whole series of issues that are maybe best left alone.
hot af.
