Going on an adventure by yourself is lonely and dull. Navi may seem “annoying” at times, but it’s hard to imagine Ocarina of Time without communication with Navi, and communication partners like Navi have been employed in different forms in subsequent games in the Zelda series. I think that how you feel when you have to say goodbye to a partner who you sometimes thought was “annoying” is an important element of the experience of Ocarina of Time.