I hate to be the first one to say this after 5 pages of posts, but...as far as what's "worthy" of being canon in terms of how fitting/explanatory/sensible the idea is, I have to say... the single dumbest idea in all of Fallout is at the very core of Fallout 2, and Fallout 3 had to go along with it. Namely,
Spoiler the true purpose of the Vaults being for human social experimentation
.
Really, if you think about it, it's completely ridiculous, makes no sense, and would have been impossible, considering the insane engineering feat that the
comprised of. I think the Enclave are excellent antagonists and deserving of a game or two (next game, my opinion, they should be relegated to second or third tier bad guys, on their last legs or fundamentally changed in a creative way). However, they could have been introduced without the ridiculous conceit about the
.
I thought it was a dumb change from Fallout 1, but hey, I got over it, and the rest of Fallout 2 was pretty cool (I think backing off the uber-obvious pop culture references was a great decision for Fallout 3, and that the location-based naming easter eggs, like in The Pitt, are a lot more mature than Fallout 2 hitting you over the head with sci fi references - bad Family Guy-esqe humor).
Since it was already a major part of the lore, I think Bethesda did great at making some interesting Vaults with backstories.
My main complaint with Fallout 3 would be the limited dialogue, much less deep than some of the stuff in Fallouts 1 and 2, and NPCs not recognizing that major events have changed things (Almost everyone in The Pitt, Nathan in Megaton after a certain incident, and lots more). Stuff like that is good opportunity to flesh out the story - an easy place to put some exposition. Come on, I know those omnipresent Bethesda voice actors are workaday 9-5 salary guys, they'd be millionaires if you were paying them by the hour
They talk about Jet being used for soldiers in Operation: Anchorage, so Bethesda has already shown they're willing to try to cover omissions a bit (it's true that they need(ed) to explain how Jet is in the east coast after the Fallout 2 stuff).
I'm hopeful about the aliens. If they go a Deus Ex-style route (pre-war conspiracies), I think it could actually be very cool. If they make it a cheap excuse for lame Fallout 2-style gags, it could svck. Destroy All Humans is already a game. Also, with those ex-Fallout developers working on New Vegas, you think they're not going to pass up the opportunity to use Area 51 as a setting? Puh-leeze.