I am a stickler for great dpads, so on that alone I'm going with the wireless Xbox One controllers. I have never, ever felt a better dpad. Perfectly clicky, perfectly concave <3. Not so much a fan of the bumber/trigger on it though, but I never have been for xbox. Or PS for that matter.
My Second favorite is the wiimote+nunchuck. You can position your two hands WHEREVER. They don't get cramped from being stuck together like a typical controller.
Third favorite? N64. Yes. N64. Find a more accurate, linear-pressure analog stick. I'll wait.
All it needs is a soft thumb cap for the stick.
Gamecube is nicely shaped, but the buttons are awful. They are mushy, from the A/B buttons to the triggers/shoulders. Plus the dpad, that thing's an absolute joke. Completely unusable. Make the buttons clicky, the dpad useful, triggers firm, and you got yourself a nice controller.