I skipped over a few pages so forgive me if someone brought this up already.
I read a few posts where people were saying that they were backtreading on what has already been established, changing how the Black Goo works and decanonizing Fire & Stone... This couldn't be further from the truth.
First of all, the Neomorphs are perfectly in line with what was established in Prometheus. As was clearly stated, this is the result of Black Goo mutating local wildlife, something that was entirely absent on Lv223 apart from perhaps those worms. What we do see is Holloway infected with Black Goo and proceeding to inseminate Shaw. His "Spore" infects Shaw with the Trilobite which could very well have burst from Shaw if it had been given the chance. Is the Trilobite a Neomorph? No. From what I can gather, the Neomorphs originate from a Black Goo mutated variant of local flora rather than a human so differences are quite acceptable in result of "cross polination". This all fits perfectly with Prometheus.
As for Fire and Stone... Lv223's Black Goo Monsters are the result of natural evolution accelerated by Black Goo on a planet totally absent of life outside of what was introduced by humans and the little Worms. We can also include alien micro-organisms that may have been spread by the awakened Engineer. The Spore Bearers, or whatever we want to call them, on Paradise are the result of an already established ecosystem becoming infected by the Black Goo and, as I stated in the above paragraph, as that matches with the effects in Prometheus it can match with the effects in Fire and Stone.
There's also the case of the unknown "Terraforming Device" discovered in the Engineer ruins during Fire and Stone. I don't have the issue with me right now, unfortunatly, but IIRC it is stated that it is both an atmosphere generator as well as a biological seed injector working in tandem with the Black Goo.
Nothing has been invalidated, the EU is fine.