Prometheus had a number of Problems, Characters were not used as much as they was in other Alien Movies, and yes we have our Characters who are there for just limited purpose... Take FORD (Katie Dickie) she also played (in SW EP8) a member of General Hux Team in a small role on the Bridge of one of the New Order Star Ships, this limited role is the same as her role in Prometheus... Where Prometheus Failed was more important Characters were not Developed well and had some issues... yes we had some not pleased with Fifield and Milburn, but Ultimately it was that Holloway, Shaw, Weyland, Vickers, and to a degree Ravel and Chance (not as important Characters) were not really that well done... or Acted to well either. Only David and Janek stood out as being well Written and Done.
But indeed their was back lash regarding the Engineers, not so much the appearance but the whole going down the route of them being Our Creators and playing the Ancient Aliens Card... this disappointed a percentage of Fans.
The Next Disappointment i feel for most fans, was there was no ALIENS so to speak, by that we dont mean NO Xenomorphs, but no actual Aliens killing and hunting down people... We only had the Hammerpede Attack and then Not so Alien Zombie Fifield, replacing the Xenomorphs of Alien/Aliens. Yes we got the Deacon but because it never did anything it upset Fans... It would be like if AC was a longer movie, where there was NO Neomorph infections until latter and the Gestation was longer and it came out on the ship but was stuck in the Med Pay until some of the Crew Returned and it escaped got shot at and Blew the Ship up, killing say 5-6 members of the Cast instead. Then we see David infects Oram, and kills Rosenthal.
Then on the Covenant David kills Ricks and Upworth and we see Oram Chest Burst and see the same Chest Buster and then we get the Credits.... Fans would be like WTF!!!!
so i think Prometheus got a lot of Flack for no Actual Aliens, not No Xenomorphs..
The other Problem is fans expected the movie to be a Prequel so we would START to uncover HOW/WHEN the Xenomorph was Created and HOW it got to the Derelict on LV-426... and Prometheus did not provide many fans enough Answers, and when they heard a sequel was to not give them but explore the Engineers more, there was a bit more Back Lash!
And then Finally you had some Fans, who wanted more Direct Clues/Prequel to Alien and see Eggs, Face Huggers, Chest Busters Xenomorphs... how did the Eggs get on the Derelict? a Queen?
so there was a lot for Fans to Complain about... and Blomkamps Alien 5 gained a lot of interest..
So FOX Felt.. Hang On... we needed to bring in (1) A Alien Monster Threat (2) Explain how the Xenomorph Eggs was Created in the First Place (3) Show the Xenomorph in some stage of its Evolution (4) maybe distance from the Engineers would-be Gods and Shaw and her Questions.
Ridley Scott was so pleased with Fassbender and the David Character, that he felt he still needed to be the Center of this next movie and throw the Curve-ball of David Creating the Xenomorph with the Engineers Bio-Weapon and for the purpose of pursuing his own Creation/Playing God and using it against Mankind who he felt bitter against.