How much of Tactics is canon is not clear, to be sure, but in a broad sense it does appear to be something that Bethesda has adopted given the references to it in Fallout 3. So as of right now we can probably assume that some type of BoS exists in the midwest. It is certainly more canon then Van Buren, though New Vegas is presumably going to go a long way to clarify Van Buren's degree of canon content.
The BoS are in NV... Its been said that they are in hiding, and that they player might have a tough time finding them.
I've played Fallout 1 many times, starting back in 1997 when it was released. I'm not disputing where the developers of Fallout 1 and 2 left the BoS and supermutants. But I'm simply pointing out that in canon terms Bethesda brought both of them back in Fallout 3 and that is now canon for the series. If you'd rather think of Fallout 3 as a seperate, yet another alternate reality spin-off of the Fallout franchise then go ahead, but you are also going to have to apply that approach to Fallout New Vegas (which also includes both groups in some form or another) since that is now the direction the franchise is going.
This isn't about where the franchise should have gone, it's about where it did go.
I agree with you here, and I do consider all of them as fractured spin-offs past Fallout 2. There is a pattern in this series that goes all the way back to 1998 when FO2 started to diverge from where the series 'should' have gone; but FO2 was like a stumbling, where as every game since has fallen completely off the path (and strayed off on their own wanderings). :shrug:
FO:NV is unquestionably a FO3 spin-off (and its been made clear that it is not a FO3 sequel, and the gameplay has been changed).
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*Supermutants, bottle caps, BoS, and the Enclave will always plague the Fallout wasteland now... as they have become an integral tool to recapture the brand's new Post Apocalyptic feel ~indefinitely. (even though such a state should never exist indefinitely ~just like Bart Simpson is a 23 7 year old year old, and Bruce Wayne is forever late thirty something). This is how it is in Character centric franchises ~but rarely is it like that in 'Setting-centric' franchises... except this time the game world IS the character, and its never going to grow up.