I think the fact that not only was there a swarm of fully developed Xenos, an Alien Queen and a completely different species of Alien, all on Earth 118 years before the events of the Nostromo, it kind of trivialises the discovery of the crew in the vast darkness of space. Part of Alien is a cautionary tale about how venturing into the unknown can have disastrous results.
Canon, in my opinion, should be sometimes subjective, rather than be at the hands of some exec trying to control a franchise. I saw fans of the Star Wars books being outraged when they were told that the books that they loved and invested so much time on were no longer considered canon. If you love the source material, by all means keep thinking of it as canon!
The said can be said when it goes the other way. When I first heard about AVP, I was dismayed when I heard Paul WS Anderson was directing. Mortal Kombat was silly fun, but not to be taken seriously. Event Horizon I enjoyed, and it was obviously because of this movie that he was handed the AVP rights. But even the premise is not something a big name director would pick up even based on it's name alone. Seeing it was getting a PG-13 rating told me that this movie was not made for me, but a younger audience, and horror and gore would be sacrificed to be replaced with tame monster mash action. This was confirmed when I saw it in the cinema. After it had finished I remember wishing the film would bomb, because I had a lot of fears that this would become the direction for future Alien titles. The film is very much like a video game - There is a backstory briefing, they enter the temple, it is split into levels, fights take place one after the other in escalating difficulty, and Lex gets a weapon upgrade before facing off with the final boss. It could be argued that this was based on the PC titles and praise it's adaption, but to me it isn't an Alien or a Predator movie and feels more like a product to make money.
If Alien 5 were to use the plot device that Aliens are on Earth because of the discovery of an Alien Queen on the ocean floor of Antarctica, I would be outraged. AVP is a stand alone franchise for me, the same way I look at the Ewok movies and the Star Wars franchise - Lesser talented directors being given rights to produce something with a known and loved movie name to make a quick buck. They don't reach the same levels of quality, get mediocre reviews and the audience knows that they are being sold an inferior product. This happened recently with the painfully average new Ghostbusters film.
I used to wish Alien 3 wasn't canon. The death of Hick and Newt was painful, making the whole significance of what happens in Aliens redundant. But over the years the film seems to have matured like a fine wine. I remember thinking what a depressing experience Ripley's final movie was; Dark, flea infested and industrial. Ripley had horrible bleak final moments, her death didn't seem to hold much gravitas, dying pretty much alone, surrounded only by faceless soldiers and a prison inmate. Even a glimpse of her old friend Bishop turned out to be another deception. But when I watch it now, I do appreciate the film, especially with the director's cut. But I know it is these irks from the fans that has led to 3 and 4 being scrapped in favour of a continuing story from Aliens.
Long story short: Decide for yourself what you consider canon. If you love AVP then by all means include it with Ripley, Dutch and Co.
