At the end of Prometheus, the only surviving Engineer is attacked by a gigantic Xenomorph in squid-like form. After a mighty battle, the Engineer is beaten, and infected by, the facehugger-like creature. Shortly thereafter we see a variation of the familiar Alien from the original films emerge from the Engineer's chest. That's fine, but it's a missed opportunity for connection. Had the previous two items been applied to this latest film - the Engineer could have been shown waking from being unconscious and walking back to the starmap room to attempt to finish what he started earlier, even with a damaged ship.
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