»Maybe this is the answer...«

Remember, the damn Wachowskis want everyone to be confused so they can feel like they are actually "deep." However, making a movie that just confuses people is not deep, it's insulting to the audience. That said:

1) Anyone else catch the line at the end where the last exile (little Indian girl) says she created the sunrise for Neo? In Reloaded, the architect balks when Neo suggests the Oracle is the "mother" of the Matrix. He describes the "mother" as a program designed to understand human behavior--thus, a program with emotion. What is the purest form of human emotion? A CHILD. The tiny line about creating the sunrise for Neo, and the fact that she was exiled from the Matrix (in the beginning she's getting on a train to go back in), tells me she is the program made to comprehend the way humans behave.

2) Of course it's supposed to be left in the air whether or not Neo lives. My opinion stems from what the Architect said in response to the Oracle's question. She asked something like, "What about the others?" The architect said they would be let free. If the others (people still hooked up) can still be alive after Agent Smith infects them, then Neo can be too.

3) The black leather is there because it looks cool and bad-ass.

4) If you have seen The Animatrix, you know humans started the war. Machines then retaliated. The machines don't want to war just as much as humans don't want to war. Every time they gave humans the option to end the war (when talking to the Architect), the humans just try to save themselves (The One in each previous Matrix was selfish and wanted to just keep living). Finally, someone came along that cared more about others then himself, so the machines could finally end the war.

5) This might be pure bull.

I'll say it again, it's not that "deep." The damn Wachowskis wanted everyone to be questioning the movie so that everyone would go out and see the movie ten times and buy it on DVD and such.

We all saw at the beginning when the movie zoomed in on the code and found fractal codes in yellow. No Matrix movie before has shown yellow fractal codes at the beginning. Maybe there is a sub-routine being executed.

When the Oracle shows up again hanging out with the Architect, NO ONE ELSE IS ALIVE, normal people that is. The Matrix has been purged, thanks to the efforts of these rogue programs. Finally, they found someone to end the war between machines and man, so that they could live in the Matrix in peace.

The Matrix was their world before the machines decided to put the humans into it. With careful planning, the programs finally ended the war by uniting man and machine. that's why the Oracle wasn't pissed when Agent Smith took her over: she knew it wouldn't last.

Neo cannot live or be brought back to life because neo and agent smith cancelled each other out, since the the architechs equation in the matrix is to balance everything out. so neo and agent smith no longer exists.