I think that without a doubt, MM is the hardest to 100%. The game is hard to beat on its own, even without getting 100%. MM just had so many sidequests and collectible items. Since there were only four dungeons, that makes there four heart containers achievable without collecting heart pieces, giving Link 7 hearts if you don't obtain any heart pieces. This game has 52 heart pieces in all, which is just crazy. There are a couple that are pretty hard to miss, like any of the other Zelda games, but overall, there are quite a multitude of heart pieces that are pretty well hidden, despite the fact that there are 52 of them to begin with.
Then of course, we have the masks. About 7 or so of the 24 masks that are obtainable are actually required to beat the game. I guess that's actually kind of a proportion if you think about it, but either way, it's no easy task to get the remaining 16 or 17. Some are pretty straightforward and easy to get, like the blast mask, but then again we have the couples mask, which has it's own sidequest that lasts the whole 3 day period, that requires you to be at certain places at specific times, and it's pretty easy to screw up one little thing, causing the whole sidequest to be restarted.
In addition to the Heart Pieces and Masks, this game has more bottles than any of the other games (I think), as it has 6 of them. The first one is easy to get, as it is required in order to save Koume. But some aren't so easy. One is part of the sidequest to get the Gilded Sword, and you have to win a somewhat difficult Goron race to achieve it. Then you have the one bottle you get in Ikana Graveyard on the final night, that requires you to lead Dampe to a bunch of different places in the area in order to get to a big poe which is killed to get the bottle. And again, there is one that is part of a painful Anju and Kafei sidequest.
Next, we have the stray fairies. Acquiring all 15 in each dungeon is no easy task. It wasn't too much to handle in the Woodfall and Snowhead temples, but it was very difficult in the next two dungeons. The Great Bay Temple is already insanely difficult to get through (in my opinion, the hardest in any Zelda game), but to go out of your way and get all the well-hidden stray fairies? Near impossible. I was never able to do it, I only managed about 10 fairies. And then, there was the Stone Tower Temple. The temple wasn't nearly as hard as the Great Bay Temple to clear, but it was still very irritating to try and get all the stray fairies. In this dungeon they seem to be the most well hidden, in my opinion, as they are worked in to all these little places throughout the dungeon, and are pretty hard to find when there are basically two dungeons because of the fact that the dungeon is flipped upside down halfway through.
MM is undoubtedly the hardest, but as for the easiest to get 100% completion, I'm going to go with LoZ and AoL, in a tie. Sure, they were two of the hardest to defeat, but you didn't have to do much more than beat the game. LoZ had a few items you had to be and 5 heart containers, all of which were pretty easy to get. You also have the two sword upgrades, but all you have to do is just find those after getting the required amount of hearts. Then in AoL, you had to get 4 heart containers, 4 magic containers, and that was pretty much it, other than completing the game.