Navi might be super-irritating, but she makes up for it by being super-useful as well.
It's a mathematical impossibility to have played Legend of Zelda: Ocarine of Time and not have heard the words "Hey, Listen!" emanating from Navi fifty bajillion times, unless you did something drastic like stuff your ears with gym socks and seal them shut with duct tape. While the urge to trap the prattling pixie inside an empty bottle and toss her in Lake Hylia is understandably strong, to do so ignores the vital role she plays in Link's adventures. In Issue 286 of The Escapist, Brendan Main explains why he likes Navi, and why you should too.
You want advice about your next challenge? Get Navi. Don't know where to go next? Ask Navi. Is there an enemy near? Navi will glow red, and tell you to "Watch out!" Is there a secret nearby? Navi will fly toward it and glow green. How many sidekicks are color-coded for your convenience? This by itself is a marvel of physiological design.
Even more fundamentally, Navi is at the heart of the Z-targeting system, which controls and focuses your actions throughout the game. Any time you lock onto a skeleton, or target with your hookshot? That's Navi, guiding your strikes like a laser pointer. Go at it alone for even a few seconds without the help from your fairy friend and it immediately becomes apparent how much she's needed. Try to attack an enemy with your sword without locking on Link just ends up slashing the wall? Clang! Your sword recoils as you flail about like a cretin. Try it again? Clang!
Without Navi, that's all the game would be. If you think about it, Navi is the real brains of the outfit, out there making the big decisions. She's there before every strike of the sword, every shot of the bow, every chest that needs opening. Forget trivial things like courage, wisdom, power - Navi deserves the Triforce of Micromanagement. As a final proof, and in comparison to her companion, she can actually talk. Forget this "Hero of Time" hokum. To an impartial observer, Navi runs the show. Link is just the opposable digits.
While the perception of sidekicks has been tarnished by ineptitude of countless bumbling idiots, Main argues that Navi is one of the genuinely useful ones. You can read more about it in his article, "Hey, Listen, I Like Navi."