MM is a very good, but weird and creepy game, especially for a Zelda.
However, OoT is "the" Zelda. First in 3D, first chronologically, and it countains all the clichés relative to the Zelda series. It also sets the plot for (almost) all the next ones: Hyrule, Kokiris, Zoras, etc. The Zelda universe had never been this rich.
But yeah, 3D is the most important reason. Think of it: you are a huge fan of Zelda, and FINALLY, you can see your favorite hero in three dimensions. That was a revolution.
I love both MM and OoT, but I can understand that someone wouldn't like those games.