As someone who apparently is a fan of Troma, I'm not surprised that the story isn't important to you.
I disagree about the story elements, but they have lost sight of even the gameplay that made their games fun, every Zelda game has to have a gimmick now (boats, trains, flying), that doesn't make them more fun, it makes them more tedious.
The last "great" Nintendo game was Metroid Prime, it was original, fun, and stayed true to its roots while completely changing the style of game from 2D to 3D while retaining the feel of the 2D games. Oh, and it was developed by Retro.
Mario and Zelda 3D games for the last decade have been gimmick-driven, (straying too far from what made the games great and fun to play. The last "true" Mario and Zelda games we got were both on the N64 (Super Mario 64 and Ocarina of Time), everything since then has either been a port of those same games to a new console/handheld or an attempt to recreate the success of those games by introducing unnecessary gameplay elements (Mario Sunshine, Galaxy, Zelda Wind Waker, Skyward Sword) that fall flat. Twilight Princess was close, but it just didn't have the charm the Zelda franchise was known for...