A lot of people wondered why the Predalien looked so radically different from the human-born aliens, whereas the dog alien from the third movie looked pretty much the same aside from some cosmetic differences. This makes sense when you consider that the DNA difference between a human and a dog would be much smaller than between a human and a life form from a completely different world.
The events of Prometheus provide a plausible explanation for why Mother was able to decode some of the distress signal in Alien.
A lot of the things that don't make sense about the Xenomorph make a lot of sense if you consider the possibility that they were designed as weapons- Hollywood Acid for blood: defense mechanism as well as the 'living battery' idea proposed in the comics. Ability to reproduce with almost any species: A perfect way of making more of them that demoralizes the enemy in the process, as well as incorporating the abilities of other species in the Xenomorph's 'design'.
Might seem horrific, but a lot of Weyland-Yutani's actions are a lot more understandable if you look at it the right way. They want the aliens as bio-weapons. Seems like a fairly typical power-hunger thing that any bunch of General Rippers would do, right? Until you think about who they might need to use them on. The galaxy has just been proven to contain other intelligent, spacefaring lifeforms, or at least it did, ones vastly superior to humanity. And they're probably still around. Even if they're not, other species probably are — indeed, given the implied shared verse, the Yautja are certainly still around. Controlling the aliens provides Earth with a guaranteed-effective weapon against any aggressors. In essence, they're looking for a trump card to insure the survival of the human race. In that context, they might still be crazy, but they're more Knight Templar types than the omnicidal maniacs that they look like otherwise.
Aliens: Colonial Marines may seem like it's Retconing things when it explains that a Chestburster gestates inside a parasitic "mock-womb" that will kill the host even if the xenomorph embryo is removed, but this actually explains something: in every continuity, we almost never see facehugged victims ever be surgically cured; surely, sheer practicality would dictate that even for a Megacorp it's more profitable to surgically extract a grown Chestburster from a victim than allow it to deliver itself in the usual lethal manner, but nobody ever does so. Even the rare benevolent "xeno-farmers" use surgical clone-lumps (non-sentient masses of clone-grown human tissue and organs) and let the Chestburster grow and remove itself from them.
At the same time, Ripley 8 having her Chestburster surgically removed makes sense; Alien: Resurrection is set several centuries into the future of the timeline of the rest of the Alien franchise.
Do you remember the scene toward the end of Alien when, after hearing the sounds of Parker and Lambert being killed by the creature over the radio, Ripley rushes to the scene and sees the bloody corpses? Look more closely next time you watch it. You can clearly Parker's dead face, but it took me several re-watches to realize that the corpse in the foreground has dark skin, not Lambert's pale skin. That isn't two corpses: it's Parker torn into two pieces. A deleted scene was to have Lambert still alive and being turned into an egg.