Maybe you were holding the N64 controller wrong, with your left hand over by where the D-pad is, and reaching all the way over to use the joystick. ;)
Nah, I doubt you did, but there are a surprising amount of (stupid) people who did just that and said, "This controller sucks and is uncomfortable!" You consider the controller to have poor design, while I think it has amazing design. Playing Super Mario 64 or any other kind of 3D platformer never felt more right than with an N64 controller in my hand.
And yeah, I could just use the Wii remote for two-button VC games, but I really hate the Start and Select placements. It would be so much better if Nintendo would allow me to remap the buttons from B-A to Y-B. Somewhere along the line Nintendo thought that wouldn't be a good idea, despite that being the button layout for most Super Nintendo games. They did the same thing with playing GBA games on the DS, and even some DS games use B and A as the primary buttons, which is frustrating.
The
Thrustmaster Wii controller has button mapping on the thing itself, but the thing looks like a horrendous piece of crap and probably not all that comfortable. The D-pad in particular looks hideous. But I dunno, maybe it's a pretty darn nifty controller. Perhaps I'll pick one up sometime.