Guerrilla Games, Naughty Dog, and Hideo Kojima's part in Konami are no where near sloppy, that's a fact.
The gamecube controller is pretty yucky. Xbox controller 2nd worst. Xbox 360 controller absolute worst. PlayStation and Super NES designs are epic!
One wouldn't be a fan if they got mad at him for this. His epic games, his preferences. But it is best to build a game around the best system especially as epic as the Metal Gear Solid series.