Not every item in TP has secondary uses. What about the dominion rod? Only has one purpose: move certain statues. I tried using it as a no-fuel lantern, but it doesn't work very well. And it doesn't have any use in combat (other than when certain statues are in the right place). And so far the "don't sink in sand" usefullness of the spinner is only ever used in the one temple. Then theres the Hawkeye, the slingshot becomes redundant after you get the bow, the horse call comes too late in the game to be really usefull, and I've yet to find an area that actually requires the bomblings. But I haven't played through the entire game so some of this may be false.
Obviously its a matter of opinion, but I rather liked the Ocarina because it was a central object that drove the game. I thought playing song on it to warp was not only significantly faster than using Midna, but also, if you can believe this, more intuitive. The human brain is good at associating senses with memory, so to me it made a certain kind of sense to tie a location with a melody. If I needed to warp to somewhere I just thought of the place, whipped out the ocarina and played the tune associated to it in my memory. It doesn't make much sense at first glance, but I can definitely say it was quicker and more intuitive, for me anyway, than pulling up a map and pointing at it. Additionally, the warp points were better layed out. TP has a warp point in N. Faron, S. Faron, and the Forest temple, which are all very close, but only 2 warp points in the desert that are pretty far apart.
Oh. I didn't mention it before, but the wolf-form/human form aspect of the game doesn't seem nearly as well thought out as the child/adult aspect of OoT. Theres a lot more they could have done here. Off of my head: items that could only be used in wolf form, collars that act like the different tunics for the human form, and an entire parallel animal kingdom of Hyrule with its own side quests, shops, and the like.