I really liked this. Like, I really liked this. :)
Part of it is the song of course, it's epic just itself. But it really does seem to parallel Chief & Cortana's story... the inclusion of the anime clips was a good idea, imo, as the focus of this really is the story and the human/machine contrast between Cortana and John, the very essence of who they are individually. The Halo Wars clips seemed a touch out of place near the beginning though imo, when the theme was still being established. They could have come later with visuals were touching on Spartans in general.
Oh and yeah, she'll be back :)