Zelda.
Though I must say, Metroid Fusion was a brilliant game. Recently finished it on 3DS, now I need to get an original GBA copy of the game to add it to my collection
. Gameplay mechanics to perfection, challenging but not frustrating (well, Nightmare boss), good story and moody atmosphere. Played Super Metroid and the original a long time ago, don't remember much anymore. Going to get Super Metroid for 30 cents soon of course. For some stupid reason I missed out on the Prime games...
That said, Zelda is pretty much perfect. Every game is unique. The least game is still good. The best game is, like perfectly put a couple posts back, beyond perfection. Gameplay is always perfect, including the games that are experimental with control schemes. It's beautiful music only adds to the vast lore attached to the franchise. All topped off with perfect intuitive level designs in every game. Even after several playthroughs, most dungeons still make me think.
Lastly, people consider Mario, Zelda and Metroid as the 'big three' or Nintendo's top tier franchises, because they were one of the first and still surviving today. Even when other franchises outsell Zelda and Metroid today, these two will still get themost media attention. They're famous franchises. It was visioned as such too; Mario was about skill, reaching the end of a level through mastery of the game. Zelda about exploration and creativity through finding and discovering things for yourself. Metroid was about action and survival, overcome vast waves of enemies in a confined space.