My personal canon goes like this:
Blade Runner
Blade Runner 2049
Outland
Alien
My starting point will always be Alien. It's my favourite movie of all time and I can't help but compare all other Alien movies or projects to that one film, or measure them against it.
Now, I love Aliens - it was one of my go-to movies in the 1980s and 1990s and I still love it - but it was a terrible sequel. It unpicked the Alien, gave it a real-world analogy in an ant hive thereby stripping it of it's horrible mysterious origins, turned them from an unstoppable killer into target practice and was more a thriller than a horror, but it's so well made and is such a great action film it's right up my alley. If I had to choose one other film to part of the canon, Aliens would be it.
Alien 3 tried to capture the mood of Alien but failed, we all know the story of it's production, but it's still a good film as it's wonderfully shot and well performed. My gripe with it is the deaths of Hicks and Newt; it makes the events and character arcs of Aliens utterly pointless and although it keeps in with the nihilistic tone of the first film it just felt like it was done for either increased personal drama - which I didn't feel at all - and a reset button so that we could have more 'The Further Adventures of Aliens!' movies.
Alien: Resurrection I simply can't get my head around. It looked great and Ron Pearlman makes everything better, but I really did not like it. The alien hybrid was just ridiculous and the cloned Ripley story was intriguing but really flat.
I can't watch the AvP movies again. They're badly made fan fiction flicks that manage to subvert everything that made the franchises great in the first place. I don't count them as part of either canon, Alien or Predator, and both franchises need to be seperated.
I quite enjoyed Prometheus and liked the direction it went in, but wasn't impressed with the way they tied in the engineers with the space jockey, with bio spacesuits and the like. It just didn't feel right to me and, again, the eldritch mystery of a fossilied alien that grew out of the chair of his spaceship was flattened. Like I said before, I measure everything against the original movie.
Alien: Covenant was a good film and I liked the premise, but David being the alien's creator? I don't buy that at all and, again, based on the original film it makes no sense. I'd like to think that he's lying and part of his malfunction is that he has delusions of grandeur, but something tells me that's not the case.
Alien: Isolation was fantastic and bought back everything I loved about the original movie. Although the story was a bit...
convenient, it played out really well, and I have no problem making that part of my preferred canon.
I feel that all of the comics and novels had hugely varying levels of quality and/or competence, so for the sake of simplicity I just ignore all of that.
So...
My personal canon is Alien, Alien: Isolation and, at a push, Aliens.
Alien 3 and Alien: Resurrection can stay together as an experiment in storytelling, or Hypersleep nightmares, or whatever you want to call them.
Prometheus and Covenant are 'reboots' of the original from a wholly new angle, with it's own story and mythology.
AvP and AvP:R is ignored completely. Saying that, AvP does have some fun bits and I wouldn't turn it off if it came on TV.