Id have to say Wind Waker took me the longest to beat, it was just so different from all the Zelda titles i had played growing up, I didnt really sit down and play it till i got the HD remake, and still took me forever. I would have to say the sailing is the reason. Unlike in other title where i could easily come across a dungeon while exploring, WW just had that big ocean and very few dungeons. Not to mention a lot of things you could do in that game had little to no explanation or Hint as to how to do it! Took me forever to find the lil sage behind the waterfall. among other things.
The only other game that game me that much trouble would have to be AoL. However with AoL, I grew up watching my Mother and Brother playing it, so i knew a lot about the game and how it played, as well as remembering how the completed some task. So still WW took me longer to beat than AoL when i finally returned to it, after years of putting it off cuz i was so sick of seeing Ganon laugh at me. But i returned and get my pride back during my lil stretch of NES games i was playing. Still no easy task though!