I am not sure if you guys know what linear actually means in terms of quest design.
It's non-linear because of multiple ways most quests can be solved and how the results can affect either your future interaction or questlines, even barring you from possible choices, endings or outcomes (meaning the replay value is pretty much high).
"bypassing large chunk of story" is nice but that's pretty much it for F3, right? It's not even comparabe to NV and it's just the benefit of having a sandbox gameplay. Besides, you can also do that in NV if you manage to pass through the dangerous fauna, that is dangerous for a reason and consistency of the said world. (which is something I don't mind at all. Level scaling in Fallout 3 and Skyrim was the worst thing ever.)
I did not make this picture and I partially disagree with the rather belligerent and biased tone used in it, but the Storyline part sums up my feelings:
http://i.imgur.com/iaTw2oH.jpg