In the original script, the character of Switch (note the name) was supposed to be male in the real world and female in the matrix. This was based on the notion of "RSI" (risidual self image). The clothing and guns they carried in the matrix were loaded before the jacked in the matrix, but their general appearance (the RSI) was created automatically by the matrix based on their "self-identity".The directors have stated The Matrix series is an metaphor for being tranny.
I think this is obviously forcing an untrue label on the past films, but if that's how the directors feel about it today, you can guarantee the analogy will be true this time around. Remember, they were male when they made the Matrix. They were "female" when creating this new version.
There's very little evidence of tranny stuff in the original films. It would have been simple to have a character play a man in real life and a woman in the Matrix world, or vice versa, but they didn't even try that (an obvious plot twist, and one that was used in the Bruce Willis film Surrogates).
I'm looking forward to Dune, though I have to admit none of the trailers are exciting at all. Maybe I'll just finally read the book instead.
But they thought it was too much for the public to accept at the time, so they dropped this angle.
They still kept hints: the RSI concept and many characters looking androgynous (Neo, Trinity, Switch).
Also, the degenracy of Zion (mixed races, lesbians and gays).