Matrix Alternate Ending?

I just recently read about one of the directors (Larry Wachowski) of the Matrix trilogy just underwent a sex-change operation.  This post isn't about that, I really don't care what he now she does with his now her life.

It just jogged my memory about an alternate ending for the trilogy that I had thought up awhile back.  The original seemed to leave a lot of open questions.  One ending that would have been a mind-frack (to put it more politely) is that Neo finds out at the end that the so-called 'real-world' in which the freed humans inhabit is just another layer of the Matrix, a firewall program if you will whose purpose is to give humans the illusion of choice and free-will.  A step further would have revealed that the real, real world in which the Matrix is set is a generational seeder ship traveling through space seeding worlds with human and earth flora/fauna ostensibly to create backup homeworlds. Such a theme would reveal ultimately that it is not machines that enslave humans but man enslaves man, a story as old as history. But another layer to of nuance  to such an overarching theme would be 'man enslaves man for his own good' i.e. presumably to save human civilization from destruction on Earth by sending out a giant seeder ship to seed the stars. This opens up all sorts of ethical and philosophical questions.  Such a theme would also add a layer to the Messianic/Hero's journey (Neo as the One who would save humanity from slavery) and the 'what is reality?' and 'what is free-will?' philosophical strains. Using the messianic theme as an example, it could be seen through the light of the story of Noah's ark.  The ark is a vessel built to save a remnant of humanity from destruction (from the flood).  As such, the generation ship can also be seen as an ark, it also is sort of a messiah to save humanity from destruction adding to the layers of a messianic theme.  But there is also a tension set up between free-will and slavery vs. salvation and destruction vs. reality and deception.  Basically, this part of humanity would be de facto prisoners on this seeder ship while at the same time ensuring salvation of human civilization.  In my alternate ending, Neo and the audience would find out the truth which would provide the much needed mind-frack harkening back to the first Matrix when one finds out he is in a vat.  But meanwhile the ending would proceed with the Architect agreeing with the Oracle that humans would be given a choice to leave the Matrix.  Of course, this is a false choice since the 'real-world' as the residents of Zion nor the machines know that it is just a firewall program designed to keep everyone in.