This is now my favorite discussion on the Alien franchise. Their opinions on the films are pretty much exactly the same as mine for all the Alien Quadrilogy and Prometheus.
As for AvP & AvP:R, here's where I stand on them:
They tie in really well to the Predator Mythologies, and then by extension to the Alien Mythologies, but I'm not sure right now how I'd connect them with
Prometheus (for reasons I believe I mentioned earlier).
AvP does a good job of expanding on the larger interaction between the three races, and creating a setting where everything comes together. It's got the Aliens being smart, and the Predators showing some early phases of their hunting. It's also a good setup of the Weyland Corporation & its interests, especially in life tied in to Ancient civilizations.
AvP:R (while a little bit of a kneejerk reaction to the first film), is still one I found to be rather enjoyable, particularly because it gives us a better look at the Predator culture that isn't matched until
Predators. There's an Elder Predator who's doing something other than hunting for trophies, he's there to take care of a failure - which is something I'd wondered about (Wolf is honestly my favorite predator from any of the films). You also get the partial transformation into a Queen (flat head and direct impregnation), which is an interesting idea although it'd be just as interesting if it weren't a Predalien. Also, you've got the Yutani 's military interests brought up. It tries a lot of things, and touches on a lot of small pieces of mythology. I think it's got the better details, but the worse film.
I do love the AvP universe & games, but Prometheus doesn't seem to fit with them. This biggest point (aside from the ambiguity of the Xenomorph's origins and interactions with Earth), is that AvP's Charles-Bishop Welyand & Prometheus' Peter Weyland both seem to overlap the "Weyland Corporation" role, but not in a way that allows them to easily interconnect:
http://www.weylandindustries.com/timeline
In my mind, in the AvP universe the W-Y merger happens really early on, when the two corporations start to pool over mutual involvement in their extraterrestrial goals, and basically become the evil corporate douchebags that become obsessive about the technology, and run all the crazy experiments that you see in the AvP Games, etc. that always consider human life negligable.
In the Aliens universe, they're both legitimate corporations with their own interests, one private sector one military. The merger happens a few years after Prometheus ends when Weyland Industries' ownership is weakened. W-Y doesn't actually get any of the specific goals involving the Xenomorph until they know what happens with Ripley after the corporate meeting in the beginning of
Aliens. They have a goal that VERY strongly involves obtaining alien lifeforms after what limited information they were able to obtain about the Prometheus mission, and it's this non-specific directive that what leads to the
Alien.
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