No game should be as non-linear as BOTW. It was so extreme that it got in the way of its own objective. While some non-linearity is necessary for an Open World game, when you remove the ability for the developer to create obstacles, the game is no longer about the journey and solely the destination. Giving the player the ability to just go from Point A to Point B without any interference takes anyway any sense of adventure. What do I mean?
Well say for example, you start a new Skyrim playthrough, learn you're the Dragonborn, and head off to High Hrothgar. So if you head there the game intended you to, you could either follow the path to Ivarstead, cut through the path to Ivarstead, or head there from Riften or Windhelm if you decide to go there first. One way or another, you need to figure out a path and navigate your way there, coming across bandits, traps, beasts, sidequests, and have a real adventure.
Or...you can get a horse and abuse the horse climbing mechanic to cut through the land and instantly climb High Hrothgar. You just reach your destination, there is no adventure. This is what BOTW does and it hurts the world.
Now you don't HAVE to climb in BOTW...but since the game focuses on the climbing mechanic, the developers plan the game accordingly. Even if you don't use the climbing mechanic, you won't have the same adventures you would in Skyrim, because the developers didn't set any up...they assumed you'd just beeline from Point A to Point B. Compare this to those rare moments where the game corals you (Zora's Domain, Eventide Island, Great Plateau) and suddenly you're on an adventure, because the developers have set up enemies and obstacles in your path--because they
know what paths you can take and can plan accordingly.
However, there's no reason the story can't be linear.
It can be. It shouldn't be. Linearity and story don't mix. This isn't a movie. You don't need heavy structure for the story. The story should be used to enhance the gameplay, it shouldn't be an annoying interuption. Non-linear games are better at implementing this, which is why Open Worlds are known for being so story focused. Linearity should be primarily used to enhance gameplay.