I'd take a 3DS MM over HD WW any day (although I honestly liked WW better). That being said, WW HD in and of itself is not a bad thing, and I'm rather looking forward to it.
Also the game cube couldn't handle a realistic WindWaker, too much water.
But The Wind Waker is still one of the best looking titles and has aged quite well, not sure the HD is required for that reason alone, it already upscales into HD and looks good.