ooo... that really is a tough one, but if i have to decide i think that
Ocarina of Time! cause it has all the zelda basics in it, Ganondorf, 3 dungeons then something happens then more dungeons, water temple, Zelda got kidnap, Link start with nothing (unlike MM, kokiri sword, shield)... plus, the time limit is a great idea and all but it makes the game less free, which why i like OoT more, you can do what ever you want, whenever you want.
MM is still a great game, one of the greatest if you ask me but OoT has things in it that make it more awesome than MM.