Considering how much people seem to enjoy the story then yeah it probably should focus on it to some degree. I have a catch to that though: on principle, if your game is about traversing environments (or exploration, if you will), fighting enemies and solving puzzles, then every moment where the player is locked from the possibility of doing at least one of those things is a compromise. You want those moments to either not intrude with the gameplay or to contribute to it in some way. Feel free to call me pretentious, but I believe that even people who supposedly "play for the story" still have an understanding and appreciation of this, unspoken or not.
I don't underestimate the value of atmosphere and story though, there's a reason Wind Waker is probably my favorite 3D Zelda. It seems to me like it combined both its world and the way it all played in a cohesive way the best even if it's arguably outdone by most other games in everything else like content density, combat complexity, dungeon count, etc. I imagine more dungeons and a less empty world could only have improved it.