I have to say Majora's Mask. There was just so much extra stuff to do, you could play that game forever, and never get bored. Also, there's nothing much cooler than becoming the Great Deity!
Legend of Zelda Twilight Princess all the way. It has more features that did not appear in the OoT game. Some I would say is swinging your sword while on Epona and a faster and a whole lot more accurate in using projectiles like bow and arrow and the gale boomerang.
Yes you are right the Alpha but most likely I conclude that TP is a bit more of a recreation of OoT with more features that are more fun to use. So it is more of a improvement of OoT and you will a lot of new and old things in TP.
Mine is Link's Crossbow training. Just Kidding. For 3D it would be Wind Waker and for 2D it would be a Link to the Past. People will obviously say Ocarina of time because it set the basis for 3D zelda games.