It's not that it sucks, it's that it's...different. I constantly confuse the X and Y buttons when I'm asked to press them quickly, and that damn Z button is placed so awkwardly for not being all that much of an important button. It has the weirdest setup for the face buttons with the A button being the center of attention and it's sidekick, the B button, then the bean buttons, the X and Y buttons, revolving around the A button.
The Dual Shock 2 is the easiest controller for me to use since it's had the same design for around 10 years. I have an idea of how a game's control setup will be like by it's genre since they've generally been proven as successful. Platformers generally use the same setup, racers generally use the same setup, RPG's tend to use the same setups that they have had for years, sports follow suit, and you get my point.
It has to be slightly changed on the GC and that can be enough to ruin it for some people. Not having equally sized buttons can make it difficult to use the buttons equally like you can on the other systems. It's generally the GC-exclusive games that tend to have the best controls because they're optimized for that controller.