I don't care what Nintendo does, it's their game they can remake it if they want to, and since it's a Zelda game, I'm certain that it would sell fine so I can't even say it'd be an entirely bad move.
However, I'd much rather have Majora's Mask on the 3DS to go along with Ocarina of Time 3D, then after we get some new games and a few years pass, then it would be a better time to port Wind Waker over to the next handheld system. I don't understand why people are flipping biscuits about remakes being a terrible thing, but really the term "remake" wouldn't even be applied to what they'd have to do to make a portable Wind Waker. Just port it, it's graphics are fine, it doesn't freeze up or lag.
Majora's Mask is the last game that would need a real "remake" since it's full of blocky N64 models, it's graphics no longer match it predecessor's, and it's full off bugs (and not just the kind you put in bottles).
They've ported four of their home console games to portable consoles (remaking the last one and adding new features to another), I see no problem with this trend continuing, I don't think it hurts anything and it's the only way I got to finish A Link to the Past thanks to my SNES dying. It's true that now we have the Virtual Console, but I really enjoyed playing ALttP in my college dorm room too, where I couldn't bring my Wii but I could bring my DS (the old kind that plays GBA games).
But here's the thing, they do NOT need to put every game on the 3DS, that is way over-doing it. Seriously guys. I would even wait for a portable MM (as I've been waiting since the DS days) on the next system if I didn't feel like it would be a complete waste to not make use of how much they've got of the game just from having OoT3D. That, and because I feel like if they don't already have part of it made they won't bother with it, and because it would be weird to have them with different graphics (as it currently is).
So since I doubt that rant made any sense and I'm too tired to try and make it, here's the point: I do not want Wind Waker on the 3DS but I have no problem with it being ported to a future handheld device someday. I do want Majora's Mask on the 3DS, but I will wait as long as I have to get a portable version of it, even if it's not for 3DS.