They should have got me to write episodes 2 & 3 I would have left many
brains fried in the process - my ending would have been that the world
the computers appeared to live in was also a simulation and that
reality was a world where computers where to slave to men and we
choose to live in the multiple layers of the matrix as one big
alternative game the we kept on changing the rules for.

End scene would have been nero (who in reality was nothing like he was
in the world we see) walking through reality. The forth episode would
then have been a big dilema about if mankind should return to the real
world or forever stay in the multiple layers of the matrix.

It would have turned the series from what was a good action movie with
some high school philosophy (episode 2 attempted to get deep but ended
up sounding very shallow) into something the first episode promised.

The pay off was all the 'the one' mumbo jumbo would have turned out to
be wishful thinking and only by doing something in his real body,
where he finds out he does not know kung fu or fly, could he ever gain
any real respect.

It's still possible to make if anyone in holliwood wants to pay me for
the time to create a treatement.

"My" sequel would have had the characters realize the war between man
and machine didn't end the way they thought. What really happened was
that man had defeated machine using their arsenal EMP's during the
second renaissance. Man then decided, not to destroy the disabled
machines, but to *use them*. Not for energy, but as computational power,
since the machines had evolved far beyond human technology at the time.

The matrix, it would turn out, ran on the machines themselves and their
higher level functions had been tricked into believing they were
actually humans in a world of their own making. Some of them might
"discover" the simulation-like quality of the world they inhabited, but
they would reason they were humans stuck in a machine-made trap. Not the
other way around.

This would solve the "humans as batteries" (aka. "energy from nothing")
plot hole. Because this way it doesn't HAVE to work. The machines that
realize they inhabit a simulation would just have to think it works.
It would also provide an explanation as to why some of the characters
could bend the rules of the simulation they were trapped in (slowing
time, superhuman strength, resurrection, etc.). Because they would
literally be the ones manifesting the "reality" their mind inhabited.

The agents and rogue programs would still be machines, but they would
only *think* they knew what was really going on.

The only actual humans in the entire trilogy would be a pair of
operators, logged into the matrix. Namely the architect and the oracle.
The "big reveal" that would end the last movie, would be a scene were
the architect and the oracle log off.
The camera zooms through the left eye of the architect as he is
dematerializing. Inside the eye everything turns pitch black for a
second, before another world explodes into being from the center of the
screen. There we see a man leaning forward in a reclining chair, the
camera centered on his left eye. Behind him another man is removing a
large headset with wires hanging from the ceiling connected to them.

Those men would be the Wachowsky brothers.

*cue credits*