I read your review, seems interesting. Although, the ProtoAlien doesn't really make alot of sense.
AvP has established that Xenomorphs have already existed for thousands of years, meaning that the creatures encountered in Prometheus could not have been ProtoAliens.
My only theory for these organisms is that, if they originated from this black goop, which obviously must contain genetic material, then perhaps, assuming that the Xenomorphs are a creation of the Space Jockey, these organisms came from leftover genetic material from true ProtoAliens made long ago.