A lot of people are mad that this movie upsets the "canon", but it was meant to. Have you ever heard Ridley Scott talk about the Alien sequels? He isn't interested in any of them. And think about what we tend to get from Alien sequels:
Facehuggers, at least one exploding chest, aliens jumping out of the darkness and grabbing someone, an android, a scene about how "oh shit they're smarter than we thought", etc.
In other words, same shit over and over. AvP is bullshit, but I know I don't have to rail on that here. Even the expanded universe, which mostly takes an Aliens approach, is pretty derivative. A lot of the comics/books are okay, but they're all kind of ripping ideas off Heinlein and other better scifi writers.
What made Alien so effective was a good cast of characters that felt real, a realistically beat up and average space-tug, and an alien that no one knew shit about. Facehuggers aren't scary when you're expecting them, but when you're introduced to the concept, it's shockingly effective.
For all it's flaws at least Prometheus had the balls to make 180 turn for the franchise. No more Predators, no more action movie where thousands of aliens get mowed down. It's becoming its' own unique franchise. The way they depicted the alien birth at the end was enough to sell me on a sequel. Instead of trying to freak you out with gore and loud noises, it actually looked like the horrible, messy birth of a brand new lifeform. I like that there's a mystery to the xenomorphs' evolution again - in a Prometheus sequel none of us would have any idea what to expect.