djrees56: I signed up specifically to reply to your comment.
The eggs in Alien are not thousands of years old. And the reason for that is the same as the reason why the creatures from the two films look different.
The eggs in Alien were eggs, containing facehuggers. The things in Prometheus were not just vase-like, they were vases, containing the black goo.
The black goo works in concert with the host DNA: goo + Engineer = humans; goo + worms in the soil of LV-223 = cobra-penis-monsters; goo + Holloway + Shaw = Nasty Mutant Spermbaby; NMSb + Engineer = the first and only xenomorph in Prometheus, the female that pops out of the Engineer at the end.
That alien was the shape she was because of the host DNA that had been part of its evolution: first Holloway, then Shaw - when she removed it, it looked like a giant mutant sperm, and it continued to grow as fast as it had within her - then the Engineer. Pure goo + Engineer = humans, but goo that has been used to make a monster - because of our DNA - can be quite dangerous to the Engineers, and it comes out of them as a humanoid-but-nasty Alien.
The Engineers were using the goo to grow new life on dead planets. They thought they were in control... but what if the goo changed, say, the Engineer version of the flu? This might be exactly what made the severed Engineer head explode, and why they had locked down the base, and why the holograms - their version of a flashing light and siren - showed them running in their spacesuits, and why there were dead Engineers in the halls, and why the one living Engineer got so pissed at the humans: they had gone to all of this trouble to lock down the virus, to contain it, burying it in 'pyramids' with warning skulls carved on top, and these humans barge in, opening doors, breathing the air, and in general being a threat to the Engineers, by their very presence, because the goo-mutated virus (or whatever it was) could affect humans, who have the same DNA as Engineers but aren't as advanced, and the disease could leapfrog up our Engineer-given DNA and become a threat to the Engineers and, eventually, to all life in the universe. Perhaps the humans should have considered that only DEAD gods reside in pyramids.
If we hadn't been there, if we hadn't come in contact with the goo, there would not have been that new kind of xenomorph... which became a huge threat to the universe, because it infected fleeing Engineers and then used a new trick it had learned when it impregnated Shaw: laying eggs all over the place. Eggs with new monsters in them, that were specifically dangerous to us because we helped create them. (And therefore dangerous to the Engineers, because they helped create us.)
In Alien the dead Engineer, the eggs, the facehuggers, the chestbursters - these are all descended from the stuff that happened in Prometheus. Humans got to LV-223 in 2093. The Nostrom got to the other planet in 2122. In between those dates, the female xenomorph infected an Engineer from one of the other ships, it tried to flee, and it crashed when a chestburster broke out of it... and went down into the cave where it grew and laid eggs. Those eggs weren't thousands of years old, they were just years old.
