if I was scripting the sequels
a) there would be no agent smith - totally no need for him
b) the machines would revive the previous 'one' very similar to how kanada attempted to revive akira.
c) the movie would be split into two parts
1. the real world with the machines trying to destroy zion
2. the matrix, with neo removing the illusion of the matrix i.e. he would fly up to a building and show the matrix code behind it
d) all out battle in the matrix between neo and the previous 'one'
the big flaw with the sequels is you never really feel a threat unlike the original movie where neo, trinity and morpheus seemed to be fighting a losing battle. neo had become too powerful and instead of making the threat rise to neo they lowered neo to the level of the threat 'hmm...upgrades'
the only thing I would have left from the sequels in the machines siege of zion which is well done, I would totally redo what happens IN the matrix and I would redo what happens in the machine world