I might be incorrect, but I was always under the impression that the stories were basically dropped and then unified into the mess of a storyline so they could rush the game out.

Limsa always looked like it was the most fleshed out, then Ul'dah looked like it had a bit of time spent with it... but poor Gridania.

I hope the main scenario gets major revamping for 2.0 otherwise I think the quality issues will really deter and upset players.