Bguy7
The Dragon Lord
They don't have to. They could still make it fairly story heavy, you just wouldn't have a lot of elements that would be sequential. For instance, you could still have evil team events in a certain area, it just wouldn't matter whether or not you do that first or last.
And there's one of my issues with Breath of the Wild. It has story, sure, but that story has no sequence of events, which ruins the impact of the story. If you can't build upon previous story elements, suddenly your options for the story grow a whole lot less appealing. For example, one of the major changes made in Sun and Moon to have a better story was to give a character, Lillie, actual major character development. That really can't happen if you can meet said character in any of ten different places in any order you want.
As I said, GameFreak does these things to ensure every child in the family has their own cartridge, upping the sales.
You said that they stopped people from using an exploit. As a video game company, it is their prerogative to fix exploits.