Thanks for posting!! There are some really interesting things in those notes. The hammerpede actually being an experiment that was ditched for a better design. I guess the one thing that I really feel they should have shown in Prometheus is how some of their advanced biotech works. It was stated in the notes how they wanted to show the engineers controlled their tech on a molecular level but in the film we do not get a true feeling of this. There are hints of it, like when David looks at the green goo up close and says "impressive", but they never show us what he even saw.
It is also interesting that at one point Huante actually puts Angels in parenthesis referring to the engineers. I thought it was very fitting that the movie went the route it did because I remember reading a long time ago that Ridley and others were staring at the alien Giger created for the first movie and speculating how it actually came to be - Ridley's response from the reflection was that it had to be a demon.... kind of strange in a pretty hard sci-fi movie but coming from Giger's art it makes sense