Do PH and ST count as 3D games? I always considered them to be 2D games.
Anyway, my favorite thing about OoT is the pick-up-and-play aspect... There's not many tutorials, etc. You just start with a couple cutscenes, and get straight into the gameplay. It's straight forward and fun, and the 3DS version further enhances the "pick up and play" aspect, which is really nice.
PH and ST are very similar to Wind Waker, but with a different vision angle.
Also, for me OOT is far better than MM.
The whole 3 days concept, in my opinion, do not suit well on Zelda franchise.
For me, the charm of Zelda franchise is exploring different places, taking your time.