For the record, I don't even have a problem with Mothership Zeta. It's DLC, after all. I've decided not to buy it, and I figure you're allowed to have a little fun with the DLC if you want. It's my understanding that Bethesda thought they'd have fun designing, and I won't begrudge them that. As far as I'm concerned, there's a world of difference between something that occurs in the core game, and something that happens in DLC. It's like Oblivion's vaunted Horse Armor DLC - you're not "missing" anything if you decide you don't want to pay for something like that, but it's there in case that's something you really wanted to have.
And sure, little green men are a part of 50's pulp sci-fi. But I think there's a difference between having aliens as a major story point, and allowing them to maintain an aura of mystery. Let's say there's an explorable Area 51 in Fallout: New Vegas, for example. I think it might be cool if you went in there and found some videos of an alien autopsy, and maybe some alien skeletons, or some poor little green man preserved in a jar. But I'd be a little bit upset if they were to go too far and take away all of the mystery surrounding their presence. It's like the X-Files, which I always thought was a more interesting show before the last few seasons where they started blowing the lid off all the conspiracies. Or the Roswell Incident, which in reality is probably a lot less interesting a story if the "truth" were revealed.
Also, you know why I'll consider Aliens to have been "canon" in Fallout 1? Because it wasn't until something like my second or third playthrough of that game before I even encountered that crashed alien spaceship. For "canon" to have any meaning as it relates to videogames, it can only refer to that which
has to have taken place. (ie, it's "canon" that in Fallout 1 Tandi lived, and that you got the good ending for Arroyo - because those two things have to happen in order for NCR to be around in Fallout 2. It's "canon" that in Fallout 3 there's a town called Megaton, but "canon" isn't particularly concerned with whether or not it got blown to bits - unless in Fallout 4 there ends up being a crater where it's supposed to be, etc.)
And the alien special encounter that started this whole gorramn thing is something that's not even guaranteed to occur while you're playing Fallout 1...
(And the whole "aliens tricked humanity into destroying themselves" theory is something I'd really have a problem with, were it true. Because that ties back into the whole thematic consistency argument again. The post-apocalypse is about humanity's hubris, and us being the deliverer of our own destruction. To have aliens behind the whole plot completely changes what the entire setting is all about. It would turn the franchise from Mad Max into something more like Battlefield: Earth - and I don't think anyone wants that to happen...
)