nu_clear_day, I see what you mean when you say "if it was that important, they'd have included it in the base game" but that actually doesn't make sense to me. By that logic, you can choose to not buy Fallout 3 vanilla and claim nothing in that game is Fallout canon simply because you didn't get it. They made it, they sold it and people got it -- that makes it part of the Fallout experience and universe. Therefore, it's canon. The only way for them to get rid of the aliens now is by retconning the [censored] out of it.
All I'm saying is that the "canonicity" of aliens in Fallout is largely irrelevant. Not only that, but we're probably lacking proper terminology to describe events within a game that's supposed to be an "open world" RPG (ie, it's nominally about each player's unique and largely subjective experiences.) I think there's a difference between what's "in the game," and things that we need to set up on a pedestal as "canon." I think I've said this before in previous threads, where the only way that "canon" has any relevance in a series like this is in reference to things that
need to occur for the continuing story arc to make sense.
In Fallout 1, for example, the "canon" story is that you saved Tandi from the Raiders and that you at least made sure Arroyo was able to thrive after the events of the game. Those two things need to be canon in order for the NCR in Fallout 2 to exist (and because if Tandi died in Fallout 1, you wouldn't be able to meet her as an old woman in Fallout 2.) That's canon. As far as I'm concerned, almost nothing in Fallout 3 is anything we need to consider as canon - simply because there's been no further iterations that need to make use of it.
And I've already said this in regards to aliens in Fallout - it's a win/win already, without having to get bogged down in terminology. DLC exists for each player to customize and expand their gaming experience as they see fit. If you want Horse Armor in Oblivion, it's there for you to purchase (or not) depending on whether or not you want it. There's no reason to bother with worrying about whether or not everyone agrees if it's "canon" that horses in Oblivion wore armor. Ditto with the aliens thing. If you like the idea of aliens, then there's already extra content for you to purchase which expands upon that notion.
However, if my character never got abducted by aliens, then I think it's safe to say that - as far as my own personal game experience is concerned - that it never happened. If Fallout 4 comes along and there's a big subplot dealing with the results of your character getting abducted by aliens during Fallout 3, then yeah - that would then become part of the official "canon" of the series. It would be necessary in order to maintain internal consistency within the open-world parameters.
Otherwise, we're talking about whether or not the presence of a crashed alien spaceship sets a precedent for aliens being an
integral part of the Fallout narrative. Yes, my characters in Fallout have come across a total of two alien spacecraft, and seen a total of 3 (two next to the ship in Fallout 1, and the one in the cockpit in Fallout 3,) dead alien bodies. That's in the game, and I don't have a problem saying that those were things that "happened."
But I'd be very suprised if any future Fallout games really expanded much terribly further than that. Much as in real life, I figure there's aliens in the Fallout world; but that they're largely busy doing their own thing. Whatever they're doing, I doubt it's really going to have much of an impact upon the core narrative. Their presence is in the game, they exist. But they're not necessary for internal consistency, therefore I don't see as how whether or not they're considered "canon" is relevant. If you like aliens in Fallout, then so much the better. I don't really see how it's important to anyone that I become as convinced of their importance as everyone else.