Okay well after beating it... there's basically no story until the last town you visit in CD1, then it slightly picks up... CD2 seems random at first but makes more sense later when they bring up the areas you visited while confronting Nene.
CD3 is basically just the final dungeon/world/area/whatever, but it was pretty fun.
Oh, and the boss music with Destroy was sure worth playing through the entire game for. I guess Uematsu still got it.
Overall it was an OKAY experience... nothing spectacular, but definitely worth playing.