(1) The black goo
The liquid is first revealed to be ingested by a human looking man in order to disintegrate his entire body and provide the building blocks for life to start again.
But the same black goo is then shown to be very dangerous - if touched results in immediate hideous changes the test subject's DNA. Canisters of this stuff are packed into the Juggernaut destined for earth. WTF? Are they trying to 'reset' all life on earth or create a planet full of hideous monsters?
Whats going on here? Is the black goo 'past its sell-by date'? Has it fermented over 2000 years from a disintegrator into a mutating agent, creating new life forms with accelerated growth rate and strange qualities, acid blood, giant tentacles etc? That makes no sense.
(2) Engineer's DNA = human
If the Engineer's DNA is identical to humans that means all the HR Giger visions and bio-mechanics from ALIEN have now officially been flushed down the toilet. It means that the Engineer is not a creature - he is a MAN. It means that all that 'sort-of-bio-mech' stuff on his body is nothing more than a body hugging garment like the one Shaw or Vickers is wearing. It means that all the incredible bio-mech design from ALIEN, body shaped starships, bones and ribcage exoskeleton stuff is all simply: cosmetic design! It could be any shape really, but that was the look and feel these alien humans wanted! Pathetic.
(3) Giant alien man in cave paintings --> creator of all life on earth
From the point of view of Elizabeth Shaw, how the hell does she make the leap from a correlated set of images showing a star map to KNOWING that these early 'alien' visitors engineered all life on Earth?
(4) Why wait 4 billion years, thats
4 billion years, to finally arrive at (what is presumably) the pinnacle of 'design' i.e. a human man (
), simply to then destroy it? If the engineers possess the technology to create large organisms at will with a highly accelerated growth rate simply by touching the black goo? Heck one of the murals shows a michael-angelo style depiction of an apparent instantanious act of creation.