I find this opinion on lack of story quite interesting. For a game with this much freedom, I think the story was bound to be on the way side as it's difficult to keep a linear-type of story compelling enough for players who play 80-100 hours into the game mostly exploring the world. I mean, I also heard of some opinions that while MGS5 and RDR2 had great open world concepts, when they tried to provide a compelling narrative, it was a bit flat as there was a sense of disconnect while trying to complete missions or playing for a certain amount of time in the open world.
You may have to sacrifice one thing for another when it comes to an open world narrative. Zelda BoTW was a complete open world game, meaning you can do whatever you want and go wherever you want to go as your imagination is the only thing holding you back. Thus, the story was built through pieces of text found in various aspects of the world or through dialogue and cutscenes/memories. Whereas games like The Witcher 3 and Batman Arkham City (didn't play TW3 yet but its just from what I heard) had great narratives, but not necessarily open worlds that you can do whatever you like (they still had directional marks you have to get to). Even Aonuma acknowledged from E3 2014, with Wind Waker, while they made a vast open world, you couldn't "cut through the boundaries wherever you like to explore [Wind Waker's] world." It may not necessarily was affected by the story, but even then the narrative was not that deep, although compelling to the overall lore of the Zelda franchise.
Play TW3 when you can.
I personally see the future Zelda games using BOTW's approach only instead of memories you get events e.g. you're exploring then you come to Hateno village and a story event is triggered when you arrive. This way the open freedom is maintained with the game being more story driven.