I would hardly consider OoT to be "the greatest game of all time". An argument can certainly be made for it being ONE of, but not THE (unless we're just talking objective "my favorite game is...." opinion).
As far as jump from 2D to 3D, OoT certainly was a massive leap and achievement, for sure. There really was no other game on any other console comparable that gen. However, Mario 64 was the real MASSIVE "2D to 3D" game. OoT may have been prettier to look at, but Mario 64's mechanics were gold, and really sold millions of gamers on 3D gaming. Which was both good and bad. Good, because M64 showed how GOOD 3D gaming could be done. But also bad, because it only further caused developers (Nintendo included) to prematurely abandon 2D gaming, just when masterpieces like Yoshi's Island and Symphony of the Night were coming out. So much more could have (and should have) been done with 2D gaming during that N64/PSX gen. But I digress.
OoT is a great game, and deserves most of it's praise. However, personally, I don't even consider it the best 3D Zelda. To me, the GC version of Twilight Princess surpassed it, in that it was a very OoT like game, but was better and had more in almost every way. No 3D Zelda has yet to surpass TP to me. We'll see if this Wii U game can, but I won't hold my breath till I actually see (and play) the final form.