I think the GDC judges confused atmosphere
because quite honestly the atmosphere in Fallout 3 is absolutely amazing. However atmosphere is not the writing, and definitely not the story. It's just the back-drop the story takes place in. Unfortunately the story itself wasn't engaging. It took itself way to serious. It didn't insert any humor found in the previous games. And I really didn't care about what happened to Dad or any NPCs (e.g. I came back to Vault 101 and killed everyone because I didn't CARE).
Juxtaposed with The Witcher and NPCs I really cared about what happened to them.
So if Fallout 3 sets the precedent for what is considered great writing then I think we're in a world of hurt for what's to come.
"Hard times create strong men. Strong men create good times. Good times create weak men. And, weak men create hard times." - Those Who Remain by G. Michael Hopf