I don't think anyone considers the AvP movies 'canon' in either movie universe. In fact, the AvP movies do just as much to piss fans off, if not more, as/than Aliens 3 and Aliens Resurrection (one of the biggies is being set modern day and not in the future with some Colonial Marines on the side of humans or just not being in space in general; honestly: Aliens was a good blueprint for what was wanted. Just add in Predators and a few additonal story tweaks would have sufficed). The movies are more just a sad attempt at tackling that beloved idea of the 2 coming together in a movie (since Predator had the nod of the Alien skull on the trophy wall). If you've read the novels/comics, the AvP movie screws with just too much that's established. If AvP had more care put into it in regards to both franchises on the big screen, then maybe you could consider them canon but that's not the case (I'm mainly talking about from the comics/books perspective in my previous post, not the movies; I just want to see what the Prometheus movie adds to the mythos in the comics/novels with the new info we have on Engineers since they were so shrouded in mystery (and still kind of are) up until now).
They really should have gone with the Machiko Noguchi storyline for the movies but I doubt they had the budget to do just as much. They pull the Human x Predator teamup in the AvP movie right from this storyline as Machiko teamed up with a Predator Leader (instead of a newly blooded one like in the movie) to try and survive in that story and she was blooded with his mark before he died which later allowed her some acceptance to hunt with the Predators herself.