[quote name='clockwork-zombie']Also I forgot what they were but there were a number of differences between the Dreamcast and Gamecube versions. What were they exactly?[/QUOTE]
Working from memory...
There was an additional side mission for capturing Moonfish. Doing this gets you alot of awesome gear, including some of the better weapons in the game.
There were also "wanted" missions, which essentially consist of new boss fights, some of which are among the toughest in the game. In addition, a new side story involving a girl who attacks you at certain parts with a scythe.