Well, in this particular case, Shinji is only in charge of the most recent "cycle", and only by accident. Both Gendo and Seele were trying to control the fate of humanity, but because Rei rebelled and refused to be a puppet, she let Shinji choose. It's a large-scale, literal interpretation of the journey each soul takes in each lifetime; in religion this journey is taken by each individual soul, and each re-incarnation is another "cycle", another step in the journey to enlightenment. When the soul finally becomes enlightened, it joins with the universe to become part of all things, to be ever at peace.
26-Jan-2005