My thought on Matrix final (sorry to use English):

Neo and the Zion had nearly beaten the machine. However, there are not enough human in the real world. So that Neo needed to go back to Matrix to save people out of it.

However, the Agent Smith process (maybe one of the bigggest Orphan process in Matrix) had spread out and taken the human out of the control of Matrix itself. So that Neo needed to take root account (had taken the Matrix machine) and kill the Orphan process in order to let people coming out of the Matrix.

If Neo chose to re-build Zion in "Matrix Reload", Machine can "reboot" the Matrix and help Neo to setup some simple "saviour world" again. ALL Orphan processes in the Matrix can be killed at the "reboot" stage. Machine got the power, Zion rebuilded, so both under controlled well, and the Machine can cover the weak point.

Nevertheless, Neo had chosen to fight with the Machine.