I have only seen the comparison of OoT 3D VS OoT64. The 3D version is better, for better graphics and gyroscope controls. (I don't care about the iron/hover boots, they didn't bother me)
I am never playing the gamecube version of Wind Waker, because many of my problems with it are supposedly...
Maybe for first timers who have never played the game before, but since i've played OoT way more times than I should based on how much I like it compared to other Zelda's, I think it has one of the worst stories.