Update the graphics for all of them up to Wind Waker, for starters. The 2D ones would still be on a 2D plane, but they would look awesome and 3D and not pixalated.
Perhaps in WW, MM, TMC, and the other short ones I would find a way to add in more dungeons without altering the storyline, because I was so sad when those games ended after only 4 or 5 temples, however they have brilliant stories so I do
not want to alter that in making them longer.
If I could make the older games have more character detail and make the story clearer in the game, I would. Perhaps add cutscenes? additional dialogue? I love how Link's Awakening has little cutscenes with varying degrees of detail, I'd put things like that in the older games because it would really bring a new life to them. And not just for the first three games, but for the Oracle games, FS and FSA, and Minish Cap too. I think it would work with the improved graphics.
Having played Majora's Mask and Ocarina of Time the most of any Zelda games, I have a few small details that I would add or change in them, like a few more reaction animations from Link at certain points in the game, and improve the over all cutscenes in both games, OoT particularly since I can think of a few scenes that really need it. I wouldn't go full out Wind Waker on the expressions but a little bit more on certain scenes, like when Link says bye to Saria as he's leaving Kokiri Forest for the first time, and when Romani get's abducted (there's no reaction at all from him!) But that really gets into my opinion, you might have thought those scenes were fine.
Ahh, finally a place to put my comment about saving...OK so if I worked for Nintendo (first off, one life goal down!
) and could change anything, I'd make it so that when you saved in ANY game (let's say I'm rereleasing A Link to the Past) and then picked up you game later, it'd pick up immediately where you left off. That's something that's always bugged me in every Zelda game and I'd LOVE to be the person to fix it!
If I were remaking Majora's Mask for a handheld I think it should have this feature. Not as a perma-save, but as as a sort of portable Owl Statue. Seeing as it's timed, and handhelds often need to be stopped quickly, I think it would really work there. Pressing a button twice is a lot faster than playing a song, watching a warp animation, and talking to an owl statue.