I'm quite annoyed to find that this has made me far more interested in the movie than I was before. So I'm going to speculate on what the 'similarity' Scott mentions might be, as well as having a stab at what the invention of the beast might have involved. Naturally, I have no idea if any of this is valid or not, but I'll try to back it up where I can.
Paradise Lost, as any number of articles can tell you, is an epic poem by John Milton about Satan's rebellion and the fall of man. It was written 'to justify the ways of God to man' which is an admirably ambitious brief, and many thousands of turgid University essays have been produced debating whether Milton even comes close to achieving his aim. Ridley Scott expresses doubt as to whether his interviewer has ever read all of Paradise Lost, and with good reason. It's a bit wordy:
'Don't write this down, but I find Milton probably as boring as you find Milton. Mrs. Milton found him boring too. He's a little bit long-winded, he doesn't translate very well into our generation, and his jokes are terrible.' - Jennings, National Lampoon's Animal House
To my mind, there are three elements from Paradise Lost that could easily be a major part of a Prometheus sequel. These are the concept of a war in heaven, the figure of Satan as heroic rebel, and the tragedy of the 'fall' of man.
War in Heaven
This aspect of the original Prometheus movie was picked up by many commentators. (It wasn't one I dwelled on myself, as I was more keen to sift through everything Damon Lindelof had ever said in my search for material to substantiate the Space Jesus theory.) In brief, there seem to be at least two Engineer factions in Prometheus. There's the robed lot with the disc-shaped vessel from the film's opening, and then the more biomechanical lot with the croissant-shaped vessel from later on.
So what we might be in for is a clash between Engineers, ideological and physical. Did one group create humanity while the other group decided to destroy it? Are we looking at a Minbari-esque caste system in which one group builds while the other tears down?
Ridley has already commented on this some time ago, referencing Paradise Lost:
"In a funny kind of way, if you look at the Engineers, they’re tall and elegant. They are dark angels. If you look at 'Paradise Lost,' the guys who have the best time in the story are the dark angels, not God. He goes to all the best nightclubs, he’s better looking, and he gets all of the birds." (The Playlist)
A 'war in heaven' story would be able to draw on mythology and archaeology in the same way that the original Prometheus did. There are legends of clashes between primal divinities in many cultures: you have the war of the Greek Gods against the Titans, the Norse Gods against the Giants, and so on. It's conceivable that Alien: Paradise Lost is presenting itself as the truth behind the human story of 'God versus Satan'.
The figure of Satan
Satan acts as a bridge of sorts between the myths of Prometheus and the story of Paradise Lost, inasmuch as the two figures are conflated in Western occultism, notably by our old chum Aleister Crowley. He explicitly identified Prometheus bringing down stolen fire from heaven with Satan encouraging man to eat from the Tree of Knowledge. The Prometheus/Satan figure, by empowering man to be more than his brute animal self, was thus seen as an initiator and benefactor; he gives humanity the power to ascend from his base origins at the expense of the 'innocence' associated therewith.
'This serpent, SATAN, is not the enemy of Man, but He who made Gods of our race, knowing Good and Evil; He bade 'Know Thyself!' and taught Initiation.'
'His body a bloody-ruby radiant
With noble passion, sun-souled Lucifer
Swept through the dawn colossal, swift aslant
On Eden's imbecile perimeter.
He blessed nonentity with every curse
And spiced with sorrow the dull soul of sense,
Breathed life into the sterile universe,
With Love and Knowledge drove out innocence
The Key of Joy is disobedience.'
Prometheus the Titan (TEITAN) was also identified with the number 666 by means of various Kabbalistic shenanigans which I'm not even going to bother going into here. Suffice to say that in occult circles, there is a continuity of identity between Prometheus and Satan, and I'm sure Ridley is well aware of it. Incidentally, if you're interested in the human tendency to find patterns in things, I strongly recommend this article on the famous treasure-hunt book Masquerade.
The Fall of Man
This is the possible theme I'm least certain of, and yet I think it has the highest chance of tying into the movie. The idea of the Fall is that we committed some terrible species-wide sin or crime.
From what Ridley's said so far, I get the impression the 'beast' (i.e. the xenomorph) was invented in order to punish humanity, and was about to be unleashed on us en masse for this massive infraction. So what exactly did we do that was so terrible? Well, that all ties back to the whole 'why did the Engineers choose to wipe us out' question from the first movie. I maintain that the most likely answer to that is still 'because the Engineers sent us an emissary to help us and we crucified him', but who knows what the truth of the matter is?
'I always thought of the Alien as kind of a piece of bacterial warfare. I always thought that that original ship, which I call the Croissant, was a battleship, holding these biomechanoid creatures that were all about destruction.' - Ridley Scott
Having watched the clip of Ridley saying 'we're heading back to why and how and when the beast was invented', I think there's an interesting stress on the WHEN, particularly when you couple it with 'heading back'. Just how far are we heading back?
One answer may be 'to the time of Space Jesus, of course' but perhaps we have to go back even earlier than that. Remember Ridley's fixation with religious history. The guy made Exodus, for heaven's sake. And if we go by the wall plaque in the urn chamber, the xenomorph was already around in a recognisable form by the time the Space Jesus events were going to happen. It had already been 'invented' with a specific purpose of destruction in mind.
So here's my guess:
I think Ridley's taking us back to the plagues of Egypt. That's what he means by bacterial warfare. The alien xenomorphs are the 'angels of death' that were created as punishers, in order to be unleashed on the ungodly: I wouldn't be surprised if Ridley portrays Gomorrah as obliterated by aliens. I'm perfectly aware that this is a ludicrous idea, but would remind you that Ridley's proposed Gladiator 2 would have involved Maximus sent back to Earth by the Gods to seek out and kill Christ, so we're dealing with different standards of ludicrous here.
So there you go. Ancient Egypt. Or maybe Sumeria. But obviously, the whole film can't be set in ancient times, as we have to find out what happened to Shaw and Totally Headless David after Prometheus. We need some explicit continuity between the historical story and the modern one. Luckily, Engineer cryochambers can preserve you for thousands of years: perhaps we'll have ancient Egyptian humans who 'ascended into heaven' turn up on the Engineer world, still alive, and bridging the flashback story with the post-Prometheus events. David could easily translate their speech for Shaw, because we already know he's a linguistic marvel. Oh, this stuff just writes itself!
EDIT: Completely forgot to note that we've already seen Ancient Egyptian Alien stuff, after a fashion. The late H R Giger created an illustration of the alien life cycle (egg, facehugger, chestburster) in the style of an Egyptian funeral stele that happens to be central to Aleister Crowley's system. It has never been used in any of the movies to date. Given that art created for the original Alien movie was recycled in Prometheus, maybe we'll finally see it used in Alien: Paradise Lost.