I think the Xenomorph got abused after Alien 3 to be honest, but the reasons for it looking different in AR was because they have a bit of Human DNA. The Original Idea for the Prequels was simple... These Engineers had a outpost on LV-426 and they had been experimenting with various forms of Xenomorph Warfare, which appeared to be Genetic Experiments using their Creation Tool (Nano-Scarabs) on a Organism that the Xenomorph DNA originated from.
Prometheus decided to tone down the Xenomorph connection but still hint that it is Genetically related to the Black Goo and Experiments they was conducting on LV-223 (change from LV-426) and these Changes were all made simply to attempt to give something Fresh compared to Xenomorphs and Queens
I think FOX should have backed some $$$$$$$$ and actually had proceeded with Blomkamps Alien 5 to give back the Queens and Xenomorphs, and allowed RS to go on with his Prometheus 2 sequel. Leaving the Derelict a Mystery but with more clues in Both Movies that would give the answers some what.
Then FOX could assess how well both movies did and then decide where to take it next based on reception of both movies and BOX office.
The way they changed it however was a attempt to please those waiting for a P2 and those wanting a Alien 5 and Alien fans who wanted the Origins explained, but Ultimately they made a movie to try and please all of these Fanbases, but they just produced a movie that never really did the job for all of them.
