I myself have decided on a rather neutral point in-between FO3's "canon" and FONV's canon. I myself prefer to call FONV, Fallout 3. And FO"3" renamed as Fallout: Capital Wasteland or something like that. On that point I consider FONV/FO3 as solid canon, and FO"3"/FOCW as semi-cannon that can be brushed away by the true sequel to Fallout 2. If you like, compare Fallout "3" to Fallout Tactics (on canon not on gameplay), semi-canon, nothing more, nothing less.
That is my opinion (nothing more, nothing less and so on), I hope other people could see this as their opinion as well as I believe it's quite a valid one.