Limsa Lominsa storyline was also really interesting with the search for the treasure of Robbenholm, the different pirate crews competing to overthrow the Admiral, sahagin's teaming up with them, and the first appearance of the Ascian which are by far the most interesting characters in FFXIV anyways.
Y'shtola didn't really hurt this story, the "We'll just stop this story right in the middle of it, won't tell you a word about it but send you to Ul'dah to do this Path of the Twelve crap." for sure did though.