I would change the ending. Peace between man and machine. Everyone sitting on a park bench with the sun shining bright. I really don't like those sappy happy endings. I would've had it so the humans barely beat the machines and they slowly free humans but know that it's useless, there are just too many people to free everybody.
I would also tone down the war against the machines. Is it just me or did anyone else go see Matrix Revolutions to see a movie in the Matrix.