I love Skyward Sword so far, but I agree Fi is annoying for a while. However, the hand-holding becomes almost non-existent at a point. As a matter of fact, I finished three dungeons thus far and I've actually had to consult Fi at one point to figure out what to do at one point; something I've never had to do in a Zelda game.
However, after those first three dungeons, I'm starting to wonder where this "100+ hours of gameplay" comes from. I've been playing for around 20 hours, and a lot of that has been faffing about in Skyloft. I have 11 hearts, which I find in other Zelda games to be a good indication of how far along in the story you are.