simple as i can get (man, asking someone to cliff notes-ize matrix philosophy is damn near impossible):
ok. the architect told neo that since the matrix they have created needs to be imperfect to hold on the the crop (humans), there is a repeating systematic anomalie that occurs. a glitch in the control. this is what leads to zion and the one. so every time this happens, the machines have to scrap it and start over. the one's purpose is to reboot the matrix for them. but each time that happens, they are given the choice to do so or not.
Door #1: restart the matrix/zion/one cycle all over again
Door #2: try to save trinity, in vain.
the architect bluntly tells neo if he chooses to save trinity he will not only fail, but that the entire matrix will suffer a systematic crash and will not be rebooted. so, add that to the destruction of zion, and you've got the eradication of the human race on their hands. the machines don't want this to happen, because they need humans to survive. but as the architect said, "there are levels of survival we're willing to accept," or something like that. and the architect knows damn well that neo, despite having this freak anomalie that makes him part of the program, is still human and therefore will choose love over logic.
Neo therefore chooses Door #2.
We do not see the end result of this by the time matrix reloaded ends.
How was that? if anyone knows i goofed up, by all means correct me.
"i don't know half of you half as well as i should like, and i like less than half of you half as well as you deserve." -- Bilbo Baggins
"what we obtain too easily, we esteem too lightly." -- Thomas Paine