The movie was a spiritual prequel... It had ELEMENTS of Alien stuff littered all over the film, it just took a keen eye and a mind open to interpretation to pick up on a lot of it.
The thing that almost everyone missed was the fact that as soon as the film came out, during interviews, Scott flat out said "This is the beginning of quite possibly a trilogy if it makes enough money". It is very evident that the film is a far off prequel in the way it presented everything. Scott did this on purpose. Since it debuted, I always looked at the film as the start of somethjng grandiose and a smaller piece to a larger puzzle. But then again, in modern society, unless the news is force fed down peoples eye holes via social media... People tend to not give 2 shite about digging for answers or explanations. Society is so use to taking everything at face value, having answers handed directly to them and no longer engaging their brains that it comes to no surprise to me that most folks couldn't see or understand how Prometheus was an actual Alien prequel... Not enough preconnected dots for most people out there.
If the Deacon didn't tie it all together for you as a prequel though, I dont know what would...