Well, Sieses, you have to consider how much of the series they had planned at the time. I mean, with 3D it sure seems like Nomura was planning things and dropping hints all along, but how long did it take to flesh out the importance of this new collection of villains? Sure, everyone seems to have solid plans in CoM, but that's what? Six of the thirteen, and they were pretty evenly divided in their interactions between Sora and Riku's stories. By KH2, you're back to one main character and two more main villains on top of the other seven in the Organization that you're dealing with, and again, there's no telling how well planned the entire series plot was at that point, so it could be that that's why you don't see enough of Organization XIII, particularly certain characters.