Except for the inclusion of Michael Bishop in Alien 3.
That's not a plot-hole, though. Michael Bishop and Charles Weyland are different people.
So much for the horned alien skulls.
In response to the "That's not a jockey skull and the Preds don't take helmets" argument, why wouldn't they take helmets? They obviously take more than just skulls, what with the weapons they've taken off of enemies, like the pistol from Predator 2. Why wouldn't they take masks and helmets as well? It's no different than American soldiers taking pit-helmets from nazis in WWII.
Name one Predator film that they took a Helmet? Now how many times have they taken a skull? How many Skulls are in that trophy room vs. Helmets?
Why would the Predator not take the skull of a Space Jockey but instead take it's Helmet? They always take Skulls in every film I've seen and every comic I've read.
Fact is the directors of the film said in the commentary that it's a Space Jockey Skull.
Now that Ridley has designed the Space Jockey's the way he wanted or envisioned then it's not accurate anymore and has been retconned.
Then again, the AVP films and the Alien films are not officially connected.
Actually officially they are connected.
As for the head being different, apparently we can accept Ridley Scott's "authorial intent" that the creatures in 'Prometheus' are the same as the one in 'Alien', but the moment we try to accept the Brothers Strause's "authorial intent" that the skull is a Space Jockey, there's a problem? Buh-wha?
There's plenty of ways to reconcile it, anyway. Maybe the head in AvPR is older, and the mask is biomechanical and fuses with the Engineer's "skull", creating the appearance we see in 'Alien'. It's really hard to dispute that the Engineers in 'Prometheus' looked different from what was in 'Alien', after all.
Alternately, perhaps they're different creatures entirely - 'Prometheus' hints at the Engineers' creators, maybe the Engineers modeled their tech on what was seen in 'Alien' in homage of their creators. That would explain why the suits, tech, and even the Juggernaut itself in 'Prometheus' looked stylistically somewhat-different from what was in 'Alien'.