As for not following the lore, Bethesda made the decision that since they did indeed own the IP that they were entitled to change the lore as they seemed fit. But they took a deliberate policy of trying to maintain the original material as much as they could in order to keep it the Fallout everyone would recognize. It's why they placed F3 in Washington D.C. far away from the events or characters of either F1 and F2, because they were testing to see if people would respond before they went about dictating what familiar characters would do.
In short, people complain about Fallout not being what it once was, but this is sillyness. 2D top down styles have not been the mainstream style of RPG story telling for a while. To expect anything but "Oblivion with guns" was just being unrealistic and ultimately doing the same kind of expectation building that most people did with Duke Nukem.
EDIT: On Chris Avalone's twitter account he says that since F3 the Fallout Bible itself is no longer canon. So invoking the lore from that is pointless.
http://twitter.com/#!/ChrisAvellone/...00464676044800
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