Personally I think OoT is overrated as well, but hear me out before you start attacking me...
I think that people think OoT was so awesome just because it was 3D, not for the playing value. If you made LoZ, AoL, and ALttP in 3D I can almost guarantee people would think they're better. They already have a better storyline and most Zelda fans who have played all (or nearly all) of the Zelda games like them better than OoT. Turn a classic into 3D, and people would go crazy.
My point is, I don't think a lot of people recognize the game as the "best", but a lot of them do recognize the 3D and visual effects it has over the classics.