But... there's nothing that contradicts anything, story-wise. Some shit looks a bit different.
True. I guess it depends on how integral the nature of the original ship and its pilot are to your own view of the story. I would argue that they are deeply integral to the original film - Scott didn't have Giger on location making bone sets or have his kids wearing tiny spacesuits because it was cheap or easy - he did those things to communicate certain aspects of the ship and the Jockey, things that he has retconned in his new film. The only argument is whether you are OK with that or not.
I'm not. Sucks for me.
The Prometheus Space Jockey gets scaled down to an embarrassing piss-poor space suit(!) containing a tall-ish bald bloke. Oh, and his genome is identical to modern humans - whatever the f**k thats supposed to mean?
The 'Alien-Evolution' Blu-Ray cover sleeve tries embarrassingly hard to hide the fact that the Prometheus Space Jockey is a tiny tot joke of a pilot compared to the original ALIEN. Of course, the scale of the Engineer is critical to the 'DNA' story of Prometheus: 'its us, its everything!'. But the irony is that Ridley Scott went to great lengths to portray the Space Jockey as a gargantuan skeleton melded to a machine in order to emphasise its alien-ness.
Ridley Scott said that he wanted to answer the question about 'who is the big guy on the chair?'.
ALIEN fans still await that answer.
ALIEN: The Space Jockey
PROMETHEUS: See that tiny pilot bloke sitting in the chair? - that's the Space Jockey that is!