I'm in agreement that the prequels destroy a major component of the mystery of the original film and subsequent sequels. However, my own personal preference is to ignore the prequels... the canon I follow is:
Alien: out of the shadows
Aliens (1986) & still considering River of Pain which I read recently
Alien 3 (sorry blompkamp; I'd never accept a retcon)
I could live with or without resurrection and sea of sorrows. And I haven't read any of the newer comics considered canon yet. But since I currently choose to ignore Prometheus, I'd imagine I'd be ignoring fire&stone too, but I'll reserve my judgement until I've actually read it. The stories from bug hunt, meh, some work for me but most not so much at all. And as far as the weyland yutani report goes, I know it's "canon" too, and I accept it as my own except for the parts which reference Prometheus, haha
With this in mind, I still find a great deal of enjoyment in the book and audio drama. And I'm hoping alien: covenant will allow for Prometheus to fit in in some way that doesn't suggest the alien was created by David just a few years before the nostromo found it, but I guess I won't find that out until this Friday!