I don't like the Manga story about Samus growing up with the Chozo. Like Anakin Skywalker making C-3PO, I find it a stretch to bring everything together. Samus and the Chozo should be separate, but she is a worthy recipient of their ancient artifacts.
I think a real cool setting for a Metroid game was proposed in a supposed "leak" a while back though: exploring the Chozo home world after it has been impacted by a cataclysmic event, half of the wold in a present-day ruined state while half of it is in the past, full of life and the living Chozo to interact with. Samus could cross through time by moving from one side of the planet to the other. The Chozo back story would be very cool.
Samus, herself, I think is best left as a bit of a mystery.
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