Obviously just a matter of personal preference, but it seems to me that Nintendo is the only company of the three to try to rectify your complaint. They have four face buttons, similar to the Playstation, but they made them different shapes and sizes (and colors) so that they can be instantly identified by touch, making them much less confusing in my opinion, not to mention that this is the stated reason for designing them this way. If you just set your finger on a random button on the PS controller or a button other than black and white on the Xbox controller you would have no way of knowing what button it is.
With only two triggers that your fingers forefingers constantly rest on it's impossible to confuse them, unlike the shoulder buttons of the PS and PS2, and the Z button (right shoulder button -- there is no left shoulder button) is shaped so differently, and is just a button rather than an analog trigger, not to mention that it is placed in such a way that it is incredibly awkward to press

, that you could never mistakenly press it when you meant to press the right trigger.
Everything about the Gamecube controller was designed to make it less confusing, because Miyamoto felt that controllers were becoming too complex. Plus, they are the most comfortable, ergonomic controllers ever made (that us, until the Wii was released, and the Xbox360 controllers
might give them a run for their money in the comfort department).