I think Navi kind of took some of the challange away. And what did bug me is how she would tell me how to open a door or climb a ladder after I have played the game so many times. They should give you option to turn her help side off and she could just follow you around for looks ^^
I dont really think they have a reason to do it. The fairy in MM (i forgot her name) was enough like her really. I never found navi annoying she is kind of cute ^^
You get used to her after a while. I just dont see why they would need or want to bring her back.