This has been answered a million times before. They are not the same game. The one on the GameCube requires the use of a Game Boy Advance for multiplayer, which is used when a player enters an area outside of the main area (house, cave, etc.). The storyline is different, and the graphics are the same as those on the Game Boy Advance version, although it does have some added effects, such as the smoke and fire from The Wind Waker.

There have been tons of threads on this before, so go search for information yourself. In fact, we just had a thread on this exact same thing in another section of the forums...talk about not looking before you post.