It's not just that a single CDs was big and cheap compared to carts, but also that you could change CDs without having to worry about having to start the game over again. Saved games were stored on the actual cartridges, so using more than one would probably not even have been possible, not to mention how expensive it would have been.

Also, I am pretty sure the small discs of Gamecube were chosen to keep load times down. Nintendo users were used to short loading times, and I think Nintendo wanted to keep it like that. Smaller discs mean a much shorter distance for the laser pickups to move when seeking for data, which leads to faster loading.