Of course, the whole story continuously fails on a basic science level.
Once the Prometheus team arrived at LV-233, found the temple, assayed the dead "engineer" and found it's genetic code to be, for all intents and purposes, human...a "reasonable" scientific hypothesis to explain this amazing coincidence, correlation and correspondence might be:
==> An advanced, space-faring alien race visited Earth within the recent past (measured in thousands of years), and interacted with our ancestors.
==> They took a few humans back with them, and augmented them through genetic modification. That is who the "engineers" are.
What is NOT a reasonable scientific hypothesis, from the evidence available to the Prometheus science team, is to conclude that the engineers were our creators, and responsible for Life on Earth.
Even presuming the artificial introducion of primordial life (self-replicating molecule / cell) to a planet...the chances that Intelligent Life would evolve is most likely pretty low. The chances that the same primordial life would not only evolve into some Intelligent lifeform, but also that the Intelligent lifeform would be identical to their progenitors' (the engineers), has such an infinitesimally low probability, as to be effectively impossible.