what about in the end Neo is part of the matrix...he's a renegade program that propogates and controls it, but cannot leave. Perhaps in the real world he's like 80 years old and bed ridden, thus being blind folded the whole time and hooked into the matrix. it would suck but its kinda interesting. lol, i dont care if you say it sucks...its just an idea. hehe
I am personally into the really sad ending.....Neo and smith fight, but somehow trin gets jacked in and she is messed the hell up by smith...killed...neo gets mad. he is also killed.....and then it cuts to the fight in zion. It turns out much like the 2nd renaissance and everyone is being poked and prodded and having limbs ripped off.....cut to the architect ....."only human"
Picture the scene - it's the end of the superbrawl, and Neo lies defeated at Smith's feet. The following dialogue then occurs:
Smith: You've fought well, young Anderson. But now it is time for you to accept your destiny. Morpheus never told you the truth.
Neo: He told me enough!
Smith: Even the details of your father's demise?
Neo: He told me you killed him!
Smith: No, Neo, I am your father!
Neo: No, that's impossible!
Smith: Search your feelings you know it to be true! It is inevitable!
Neo: NOOOOO!!!
Thus paving the way for The Matrix Retributions. It makes perfect sense when you think about it.