To me the story must be a bit linear, or there must be fixed points in the storyline, that when you get to those places the whole story changes. So depending on how you play through the game, the story changes too. But nintendo doesnt like to do anything like this.
Since that would mean a really overcomplicated story like. By letting things get changed in a linear way, they ensure that the story goes right, and not that people get to places to keep influence the story and allow a new side from the story. Like it would mean that it would never stop, since every action has a result, it would mean dozen of storyline changes just to reply to the earlier one.
Its not really what would be a great idea. Sure oblivion, just to come back on that, is doing it way better, but zelda is very different from that game. Its also based on a legend and the atmosphere cant be said to be similar as oblivion too.
Its never the idea to make zelda full non-linear since they want control over the story, just to tell us it the right way. With too much intereferance it would require more indepth in the story where actions get a reply.

I find it rather distubing to hear that you compare the non-linear plot of zelda with games like oblivion and metroid. It is way out of place. You make up for it to say that the LOZ did it a bit better. And Alttp was getting a bit more worse.