Majora's Mask was by all means a great game, but as some have said before me, it didn't really feel like a LoZ game. I didn't like the fact that all my arrows, bombs, rupees and other stuff I had hoarded disappeared (well, 'cept the banked rupees) every time you went back to day 1.
And well, to put it in a "ranking system" like you did OP, I guess it'd have to go
- Ocarina of Time
- Twilight Princess (The "hidden moves" and new combat made it freakin' awesome imo.)
- Tie between Majoras Mask and Wind Waker.
Wind Waker would have won of the two if it wasn't for it's long ass sailing from point A to point B hauls, and the goddamn "find all the pieces of the Triforce" crap...