A is the storyline. The number is the disciplines. So 1 is battle classes, 2 is DoH and 3 is DoL.
He's pretty much trying to say that it would detract from the story to have beaten it on one class type then go back and experience it again on another type. His concern is the timeline wouldn't make sense to the player since Final Fantasy is a "one character can play all classes" kind of game. I think this is the reason he starts out talking about games where you're locked into a class from the start.
Multiple takes on a single story arc would make sense because it's a different character each time, but FF needs to have a different approach to it.
