How on earth did you have so much trouble with the Nintendo 64 controller? Yes, I admit that the only way to design a game around the controller resulted in a large waste of space, but most games either had you use the D-Pad or Analog Stick, never both. If the stick was used, the Z button was used as a replacement for the L button. I admit that I didn't have a very large N-64 library, but I've never had a problem with any of the games I've ever played with it.
Now, my favorite controller would have to be my PS2 controller. It's a third-party one, but it lights up (slowly changing color in a pattern as you play) and has rather hefty rumble components in it, providing a comfortable amount of weight to the thing. Also, there's a vertical difference between the L1/R1 and the L2/R2 buttons, with the lower buttons contoured to better fit your fingers.
A close second would be my old PC controller, which still had the contoured and repositioned L2/R2 buttons, but there was a lack of weight to the thing, and no rumble feature. It was comfortable to use, but provided no feedback and felt as though it would break easily when used. My cat ate through the cord, and I have to use a new controller I had gotten a while ago that has more weight and rumble feedback, but no contoured/repositioned buttons. However, the L2/R2 buttons are analog, so they can sense how far they're being pressed. Unfortunately, they don't work well with Joy2Key or emulators because they're recognized as a third control stick, so you can't press both at the same time.