[SoLiDUS]

It's a catch 22: Zion is destroyed no matter how you look at it.

If he chooses to save all humans: Zion is destroyed, he chooses people to
"re-populate" the new Zion and the Matrix is then reloaded.

If he chooses to save Trinity: Zion is destroyed, the Matrix is not reloaded,
killing all humans. The machines already have a contingency plan in place
if Neo decides that his love is more important: perhaps they have a back-up
Matrix with a few other humans somewhere untouched by the present Matrix?
hrmm...