Breath of the Wild is not sized up for it's story in the same way The Last of Us is ... let's be honest, a Naughty Dog game with a mediocre story is a huge blow, a Nintendo game with a mediocre story is expected.
I personally think that The Last of Us has a great story despite the fact that I don't view it as very innovative.
I think it's more a matter of story being front and centre in TLoU while BOTW prioritizes exploration and mechanical experimentation. Story tends to be the steak in Sony's first party efforts while in Nintendo's its the side garnish.
Breath of the Wild is just an iteration to a design philosophy which has brought Nintendo success for several gens so they are not the same.
BOTW's design philosophy is not just an iteration of previous games though, its a complete overhaul that plays unlike anything Nintendo has made before.