I also think Prometheus and Covenant were killing the mystique of the Xenomorph. However, Free League has done a very good job of getting the black goo from those movies interesting, so I would recommend you to watch them again to pick up ideas.
When I first saw the new movies, it seemed as if the black goo was the source of the xenomorph (perhaps that the alien-creature David created in Covenant was the original xenomorph).
In the xenomorph chapter from Free League, it more seems as if the black goo is a derivate from something the xenomorph queen can produce ("royal jelly"), and that the Engineers was just another bunch of schmucks trying to weaponize the biology of the xenomorph, and killing themselves in the process.
The creature David creates in Covenant is called a Praetomorph, and would be some sort of reverse engineering of the real Xenomorph. It's not as badass, and more stupid.
Another annoying thing with Prometheus is that the Engineers are portrayed as the creators of mankind. However, Shaw could be wrong in her assumption that they are (she bases this on similar DNA to humans). In my campaign, the Engineers could be stone age humans picked up by some other Alien species and genetically modified. Also trying to look like the these Aliens (the derelict pilot from Alien I).
All in all, I think the ideas in the new movies are good for an RPG, at least from this point of view.