Prometheus is one of the greatest Sci-Fi movie because primarily its a Concept-Rich movie. It expanded the Alien universe & explored many ideas on several scales and delivered an intriguing adventure drama more than a thriller/horror action. Prometheus was full of these alluring things:

A. The Visuals and the virtual experience; as Ridley Scott said "the cast could have slept and effectively "lived" on the Prometheus interior set during initial filming, this didn't happen due to health and safety precautions.", we all know the ship interiors and visuals of the movie were mesmerizing. This alone let the audience right into the crews' shoes. Ofcourse 'Alien' also gave a similar experience.

B. David. Unlike a unidimensional character, Scott carved a complex robot with vibrant emotions & actions. From bearing curiosity of child to nobility towards his master to cunningness towards someone who he dislikes. Fassbender pulled it off such a way that with his limited moves of facial expressions, one can readily relate to his emotions.

C. Imaginative futurist concepts which we never seen before: Prometheus spaceship, Lifeboat, Weyland's hologram recording, the Medpod, Pup scanners, Escape pods, Rovers etc. all of them beautifully designed. All of these took the audience even closer to the experience and adventure.

D. Layered characters & story. From Vickers' greed of taking over the company, her disdain from not being a wishful daughter, David & Vickers' sibling rivalry to Shaw and Holloway's different outlook on faith and god etc. All of this in an alien movie! Hats off to Scott!

The events of the story were consequences from the clash of different agendas of the characters. Vickers didn't recruit the best of the scientists (except a great Pilot, the decision which ultimately backfired at the end to her own self) because she wasn't wholeheartedly supporting her father's mission, a demanding Weyland, Fifield who was only there for money and was more of a puppet of Vickers and David who deviced his own rules to explore the place for his curiosity as well as reaching Weyland's goal.

You may term it whatever you want, may be a projection of human hubris or neo-norisque cynical archetypes, Prometheus had more memorable & unique characters than any other Alien movies.

E. Space Jockey & the Juggernaut. None of the sequels ever tried to explore the Space jockey world. All they did was deal with Xenomorphs and Xenomorphs only.

We all know that the scene with David exploring the hologram of engineer's navigation system itself is one wonderful moment of the movie. This is were we should realize why Scott sweep away the Xenos from the script and filled it with such alluring moments with only subtle reference to Alien like the Hammerpede, a very well designed off-wordly creature - just a simple worm mutated with Xeno DNA.

F. The Med-pod scene. Nuff said!

G. Rolling spaceship scene

H. The whole biological lifecycle madness resulting from the dangerous black goo mutant accelerant. David spiking Holloway --> Holloway's sperm mutated ---> Having sex with Shaw ----> Shaw conceiving a tribolite ---> Engineer getting facehugged ----> Chestburst of a deacon, an end with the iconic reference to Alien.

It also expands Alien universe to many consequences & possibilities pushing the overplayed classical Xenomorph as just one of the many diversions.

I. The mysteries and questions to discuss & ponder upon. The movie & its ambiguity has triggered lot of discussions which even today people engage in.

Unlike 2001: A Space Odyssey which ends with a big answer (next step of human evolution), Prometheus unapologetically ends with a big question.

People who dislike it are labelling it as an 'incoherent mess' just because they didn't get answers or are the ones who also happen to not have paid attention to so many things (for instance, Vickers and Shaw turning a sharp 90 degree turn at one moment and not just running in straight line) or are downright stupid (such as expecting the 2094 medicines to today's standards)

J. Finally, the movie's ability to render better repeat-viewing experience.

With Prometheus, Scott was getting away from Xenomorphs, a creature which has been overplayed as hell.

Alien: Covenant will be the last film with the classical Xenomorph in it. A:C will also explore other creatures & possibilities. The classic Xeno will only be there for fan service. And THEN, for the sequels, Scott would go completely in the new direction hence stopping the Xeno fan service once and for all. A smart move.