I think the difference is in the graphics, with the Gamecube version being better quality. Other than that, the game is the same. Where I am, it's much easier to find a Gamecube version, but it may be different in your area. Both versions have the Extreme Battle mode.
There is a difference between the N64 version and other versions, because the N64 version has the EX files (which explain more of the background information and add to the foreshadowing of 3, C:V, and 0). It's lacking Extreme Battle mode.