Moombas were in the chocobo racing game as well, if I remember right.

My guess would be that Moombas are too closely linked with the Shumi tribe from VIII. Part of me almost wants Moombas to only exist within the world of VIII and to have them only appear as a sort of easter egg or reference (like the Moomba doll in X and X-2) or in a game that returns to the world of VIII. That is not to say I want an VIII-2 (unless it's a prequel which follows Laguna), but something along the lines of the Ivalice world in its multitude of games. I just really like the world of VIII and how Moombas fit into it.