It's not an issue of how "mainstream" they are in the sense that you're thinking. It's the fact that they're so accepted as a necessary part of things now, so expected now. Really, ask yourself: why would you prefer the original ones, even if in most places having them there in any noticeable capacity (or having them there at all) would make so little sense? Every time they copy+paste original west coast (which are now, I suppose, also east coast) factions onto another part of the map, the world is going to feel a little smaller, a little less believable. There's no good reason to have the Brotherhood (for instance) in a region when it would be far easier and more logical to justify the existence of a similar paramilitary group instead, one more tied into the local setting. And why does it have to be supermutants, when there are so many other interesting (and, if you must, functionally similar) dangers you could feasibly introduce into a world whose entire pre-war military-industrial complex was focused on advancing the frontiers of NBC warfare, unconventional infantry support, and robotics?
The longer it takes Bethsoft to ween people off of core-region factions and entities, the staler the world will become and the pissier people will be when they do eventually branch out into making the east coast truly their own setting. I'm hoping they realize that, and that most fans of the more recent games do too.