I really liked the Gamecube controller, it was simple and had enough buttons. Usually. It had a clearly defined purpose for each hand, and easily accessible positioning for the B,Y,and X buttons whose shapes made them easier to push simultaneously with A (not so much with each other) and could be recognized easily by feel. I know It could have used a left-side bumper, but that's all I'd add.
For any controller, I don't think there's any reason to have more than one set of bumpers in addition to triggers, it muddles things too far and confuses the hell out of me to have to remember what they all do (pet peeve of mine).
Now - different functions need to be better applied to the controller with a proper hierarchy, something the wiimote handles well (as a trade off for awkward secondary button placement) and if there are too many button-needing commands, a better gameplay system may be in order. I like TF2, which is technically played on a controller with tons of buttons, but is controlled with only a few for most of the time, and supplementary actions are allocated to a separate system of choice rather than having too much to choose from (though you can set it up otherwise if you choose to, I know).
I've never liked the PS3 four-button configuration (the part with the triangle and the circle and all) because the setup doesn't facilitate intuitive button-switching,i.e., for someone unfamiliar with the controller, the buttons, because they all feel the same, get you into a "locked" position, where your right thumb forgets where the adjacent buttons should be. And they're far enough apart that it's hard to press them simultaneously, and I'd imagine small-handed people have an even tougher time with that. The placement of the 360 buttons seems a bit better (which are not only bigger but closer to each other), as the topmost button seems like a supplementary button to the three main lower ones, with a clearly defined center button among them, (in other words, your finger stretches directly upwards a bit to push Y, and automatically resets it the neutral "A" position when the Y pushing is finished).
Finally (and I bet PS3 owners will think I'm crazy), I really like the size, placement, and non-symmetry of the Gamecube controller's C-stick. The left joystick is the primary method of interaction for one's left hand, but for the primary action of the right hand it is not. They shouldn't be symmetrical, because a left-side joystick and a right-side A (or whatever) button are of equal importance. The 360 understands this, as did the Gamecube. The Cube and the PS3 have better placement of the start and select buttons, though, which allow for easy access to menu and pause-based functions, usually equally necessary in terms of their need to be pushed quickly (pausing can be a big issue), but need to be dislocated from the other buttons so as not to confuse gameplay and options. In this way, I'd say the 360 has these too far away.
Disclaimer: yes, I personally owned more Nintendo products than others. Yes, I've sufficiently played with the other controllers to a great degree, my suite common room had the other consoles too. Yes, the owners of those consoles agree with me. Yes, I like the Gamecube controller more than any other. Most importantly, the above are statements of opinion, not groundlessly claiming to be facts.
Summary: the main confusion surrounding controller deals with a lack of button hierarchy. Ergonomics and button quantity are practically irrelevant. This is why people are willing to pick up a wiimote and nunchuck more than any other controller as a beginner - the primary buttons are obvious. A controller that seems foreign will be a controller that clouds the importance of the different buttons.
