Majora's Mask was especially compromised due to the 4MB expansion pack requirement when the game was on the N64 -- IIRC that threw an even bigger wrench in making a good emulator. That's why the beginning cut scene to the game is scaled back on the GC, and why the framerate is even worse than the N64 version (try the Goron race especially...nearly unplayable).
Also, the emulator was made by NST. *COMMENCE NST HATE*