It seems to be a mutual feeling that Navi was somewhat aggrevating. Maybe not the first time around, like when you didn't know what to do or how to do something. But the second and third time through the game, whenever you already had beat it, she still tells you things. Of course, this has to happen because its how the game was set up. But I think in the future, there needs to be less sidekick helpers, as Lenora suggested. Since Navi herself was in OoT, one would assume that in another Zelda title, unless it took place around the same time as OoT with the same Hero of Time, Navi would be either dead, or whatever happens to a fairy when they are supposed to die.
Now, what I think would be a good thing for the next Zelda to try out is a Training Mode. Maybe they could include a sidekick in the game, somewhat like Midna, who was more a part of the storyline rather than a random fairy, but not one that tells you every move to make. The Training Mode would be an option at the main menu, or the menu whenever you make or load a file. Sorta like many fighting or wrestling games have. Training would take you through a simulated dungeon that would show you basically everything you need to know as far as the basic controls of the game. This mode would be optional, and it would save a lot of senseless help you would recieve from a partner in the game, also making the challenge of the game a bit more difficult.