I didn't see anyone pick up on it yet but if you read the article from the Independent Source 2n you will see that the original directors who were brothers (Now sisters) intended the Matrix to be about transgender issues but no one would buy it at the time. Does this mean we will see more of this issue in Matrix 4?
I could see this in revolutions a lot and thought that the director's own lifestyle was coming to light in many of the darker parts of the Matrix. If they do have that issue in Matrix 4 then I doubt anyone would be surprised by it since we were already introduced to the concept of tight black leather.