And I'm not seeing how BioWare would be better considering that their developers prefer linear stories over gameplay, David Gaider came out and said this himself recently. BioWare would be one of my last choices for a Fallout game.
I don't honestly see Bioware as any more linear than Bethesda in any particularly meaningful ways. I mean, let's compare Fallout 3 with Mass Effect. Both had a pretty fairly straight-forward Main Quest line. But Mass Effect did have multiple outcomes for many of the stages along that MQ. None of those really changed how the overall story played out, but there were subtle differences depending on what choices you made. (ie, in Fallout 3, you finish a section of the Main Quest, and there's really only one outcome for that piece - you move from A, directly B with only one solution possible. In Mass Effect, you move from A to either B, C, D, etc - even though regardless you still move on to D.) Ostensibly many of these choices in Mass Effect 1 will have an impact on how Mass Effect 2 plays out (though exactly how that works will remain to be seen - I'll believe it when I see it.) Both are pretty linear stories, but there's actually more customization available in Mass Effect than in Fallout 3 - it's effectively at least somewhat less linear than a Bethesda game.
FO3 has a number of free-roaming quests you can encounter, to explore at your own pace. But Mass Effect has those as well. Both have a number of different outcomes available, the effects of which don't really influence much in the game beyond their effect on your character's Karma level. Sure, Bethesda places all these locations on one game map and allows you to explore all the intervening areas and find lots of interesting details and small emergently narrative moments. And they do provide a much wider variety of places to discover (Mass Effect recycling the same few buildings with different arrangements of generic crates.) But they're really not so much different, in mind - and certainly equally linear (or less linear if you prefer) as far as I can see.
Sure, it's all a matter of preference. I think it's safe to say that both Bioware and Bethesda are exceptional studios that put out consistently remarkable games. But if we're talking about linearity, I'd actually say that Bioware would be the way to go in terms of non-linear gameplay. Not only can you pick your own path through the Main Quest line, but you also get to decide in which order it plays out in, which even leads to minor differences in the way that the story is told.