All the story's are crap; Aqua has probably the best, but half of it...maybe more, is her trying to catch up to the other two retards. Really, like with any KH, you're playing for that "middle" part, and the ending drama. Otherwise, their tales can be summed up in a sentence, because story-wise, the Disney stuff is just filler and a selling point.
I thought the first two had a really good story...
And I kind of liked 358/2 Days story if I remember right.