Umm there's not too much difference in terms of the job system itself but some of the Jobs have a couple of their abilities improved or dropped completely. The Dark Knight (or Mystic Knight it think it was called) can no longer use level 1 white magic, for example. Also the Ninja and Sage Jobs have had their power cut considerably to make them more equal to the other jobs. They still have their merits, but they're no longer the only two jobs you'll have at the end of the game.