As for why the Engineers wanted to wipe out human kind. I suspect they were developing a biological super weapon, hoping to use mankind as the basis for creating it, or at least testing it out. The alien always takes on the characteristics of the host it infects. Infect a bunch of dogs, they come out a little different. Infect a human being, it comes out adapted for human beings, with high intelligence. Of course, those were the latter Xenos, the end product. The messed up though in accidentally getting infected themselves. Probably on the Derelict that the Nostromo found, the weaponized DNA had gone its full course, leading to an Alien Queen who laid the eggs.
(I really thought she was going to ask to go to the alien world to throw their weapons back at them, in a last great act of defiance. THAT I could have respected!!! Not once in the entire movie did a single character make a single decision that I could have agreed with or admired. Utterly pathetic writing.)
Dare I add in the spoilers of the trillionaire who assumes that "meeting his creator" will automatically result in his creator saving him from death, even though his creator created him to be mortal? How about the science crew that doesn't seem to know the meaning of the word "quarantine" on a foreign world? (This horribly bad re-hash of Alien seems to forget that each of the Alien movies had quarantine issues in them.)I vented to my siblings for an hour about the myriad of stupid scenes and lines... and Ridley Scott's promises that this is NOT a prequel to Aliens was squashed pretty nicely at the end when the Alien with a mouth-inside-a-mouth came out of the humanoid's chest cavity... UGH!!!!