Of course, the nature of the horror at the heart of the Alien, Predator, and Prometheus films is quite different and if Fox wants to take a page from Marvel and build a cinematic universe around the films it would do well to remember another part of Marvel's playbook: each of the Marvel films has its own independent style, while maintaining certain overarching themes and characteristics. Iron Man 3 is a straight-forward action movie: RDJ's Tony Stark would easily fit in with the likes of John McClane, Martin Riggs, or Roger Murtaugh. The Winter Soldier is a 1970s-style political thriller taking its cues from All the President's Men and 3 Days of the Condor. Guardians of the Galaxy is a feel-good space adventure. They're all superhero films and they all share certain elements like snappy dialogue, straightforwardly heroic characters, but they also stand out individually.
Fox should do the same when it comes to its Alien, Predator, and Prometheus films. While each film needs to be scary and/or thrilling, they don't need to approach the subject in exactly the same manner. Indeed, they shouldn't. Each set of films really represents a different kind of horror.
The Alien films are perhaps the simplest to pin down: they're monster films and they're all about how terrifying and deadly the Aliens are. The Alien's the ultimate representation of the boogeyman or the monster under your bed: it will kill you just when you let your guard down and it will do so in a way that leaves you screaming until your last breath. They strike at the primal fear of being devoured by predators that still lives with us, millions of years after we've become apex predators ourselves. Beyond that, they also represent body horror, particularly that dealing with reproduction, and are a horrifying caricature of our society's anxieties about sex and pregnancy. The Aliens don't just eat us: they rape us first.
The Predator series, on the other hand, are slasher films. While the Aliens pursue and kill us because they need to, because it's their nature, the Predators do it because it's fun. Humans aren't food or even reproductive vessels, they're literally game, pursued for the thrill and the challenge of stalking prey that can fight back. And, as in many slasher films, there's a strange appeal to the killer(s): they're frightening and sadistic, sure, but hey, they're clever and have a code of honor. The Predators appeal to the same part of us that is simultaneously terrified by and enchanted by serial killers, that romanticizes characters like Hannibal Lecter and Dexter Morgan while still fearing the stranger in the night.
As for Prometheus? Your first clue should come from that fact that Guillermo del Toro was worried the first film in the series would sabotage his efforts to film an adaptation of At the Mountains of Madness. Prometheus is all about cosmic horror, also known as Lovecraftian horror. It's important to remember that when Prometheus starts, the main characters are fairly optimistic about what they'll find—or in the case of Vickers, disinterestedly pessimistic. No one expects to find a horror house waiting for them and no one expects that Shaw and Holloway's hypothesis about the origins of humanity would turn out to be horribly right. The Engineers created humanity yes, but their intentions are not benevolent and they are not the gods Shaw was looking for. And the mission's attempts to find answers only leads to death and madness. Prometheus, done properly, is Call of Cthulhu with a side of 2001, reminding us that those things which inspire awe are often awful as well.
Alien vs. Predator, should Fox choose to revisit the concept, should be predominantly horrifying in its own, unique manner as well. While the earlier two attempts at the crossover largely focused on the titular monsters carving each other up a better film built on the same idea should examine the human consequences of their conflict more thoroughly. The best of the AVP comics note how catastrophic the war between Aliens and Predators are to the humans who get caught in the middle, incidental bystanders who get swept up in a war that really isn't about them. Really, a good screenwriter could turn the AVP concept into a tense and harrowing parable of the horrors of war and the suffering those who end up as collateral damage inevitably endure. Consider the battle scenes of Children of Men or the horrific violence of the film Fury and add xenomorphs, Predators, or Engineers on top of that and you get an idea of where a film like that could go.
