[quote name='b3b0p']The analog stick on N64 blows ass. Your controller will probably break a dozen times over just to beat the game. I'd go for the Gamecube / Wii with Classic Controller.[/QUOTE]
I always felt that the N64 controller had the best design of any controller. Its three-pronged ergonomic design fits very well in the palm of your hand, with the Z button perfectly aligned with your index finger. I agree that the joystick would get stuck after a while, but I was able to take mine apart and clean/fix them easily enough. My friend had a problem with his controllers, but he abused them for a good 15 years playing Smash Bros almost nightly. OOT/MM aren't the types of games you'd break your controller at, anyway. I much preferred it over the GC/Wii Classic controllers.
I say stick with the original N64 versions of both. OOT 3D is good as it has 3D graphics and Master Quest added in, plus a fluid touch control system, but it's still the same game and on a smaller screen.