I'll answer in spoiler tag to the question were the story is controversial:
I do not know where to start? Maybe at the point that Zodiark gets burnt in the middle of the addon. Meteion appears out of nowhere. The second part in Labyrinthos were mostly soulless filler quests. Doomsday was really well crafted and the menace was palpable. However, what I really missed was that apart from Thavnair and Garlemald, no other areas were really affected. I hoped to see a fight between Zodiark and Hydaelyn, in live or as echo. Also, the pacing of the story was very slow at times. Overall it felt to me like they wanted to tell the story of two in one addon. Which in itself is a contradiction in terms as the story still felt slow.