[dreamless]

Hmm... I think it's like

Spoiler:

After the world got destroyed and engulfed in an egg, Ayato become the Sixth Sun and God of the Aztec religion, remaking the world with what's left, thus making a new world with his design. So the Ayato and Haruka in the ending is not the original Ayato and Haruka in the series, but the new Ayato and Haruka made by Ayato the God. I think Ayato did not reset the world as if nothing has happened, as hinted by the painting of the skeleton of RahXephon in the end