Oh, really? Usually people who have been playing zelda games for a while will say that OoT or MM is their favorite, while those who are new to the series prefer Twilight Princess, or at least that's what i've gathered from online forums and such. And real life friends, of course.
I think that MM is really popular because it is so vastly different from any other game in the series. It has an even more intricate time system than in ocarina and allows you to do even more to manipulate time with the ocarina. It's also more side quest oriented, so i'm sure some people prefer that as well. The plot is more in depth, but also more confusing, as it doesn't seem to fit in with the rest of the series. It is undoubtedly the darkest zelda game of all time, and some of the masks are downright disturbing, as well as places like the music box house. The downfall is that there are only four full-length dungeons.
OoT is considered the best game of all time for its miraculous transition from 2D to 3D, as well as tackling time travel all in the same step. With this game came the first really in depth plot in the series as well as a cast of unforgettable characters, and possibly the best music in any video game in existence. It is also the first game to allow players to learn and memorize songs to play, on the ocarina in this case. While past games did involve musical instruments, none required you to learn different songs yourself. The game also flows very nicely between the two time-periods and has a very innovative control scheme for the time, after the huge leap to 3D. And no game ending has ever made me more emotional. I cried.
