Yeah, the "crashed alien spaceship" gag is only good for so many laughs. I don't think that's something we need to inevitably see in every single Fallout game made from now on. Other than that, there already is a http://www.gamesas.com/index.php?/topic/1078258-aliens-are-canon/page__st__120 thread over in the Fallout Universe discussion, so I don't want to drag all that hullabaloo over here. (Though quite frankly - like "immersion," and "engine," "canon" is one of those terms which the world would probably be a better place if it had never found it's way into the mainstream gamer's lexicon...

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Anyway, I think it's kind of a fine line. To me, it's simply a matter of relevance. A couple of winky winks to a previous alien presence (I wouldn't mind coming across Area 51 and finding some alien autopsies or something,) is one thing. But I feel it kind of belongs in the same category as the nods to Pre-War civilization - it's pertinent to see where we came from, and how we got to our present situation, but otherwise it's just not relevant to the narrative at-hand. I voted "behind the scenes." That's just how I prefer my aliens in the Fallout world.
Another way of putting it is - take Fallout without aliens, and you have A Body and His Dog, Mad Max, The Road, etc. Put aliens as a primary plot device into Fallout, and you end up with Battlefield Earth (and I don't think anyone wants that...

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Edit: But I don't think there's much chance of any of that happening in regards to Fallout: New Vegas, personally...