I finished the 3.0 set of quests of Heavensward last night. I liked Ishgard ever since the tail end of ARR because of how dedicated and loyal Ishgardians are, but with Heavensward over, I think it will be quite exceptionally challenging for Stormblood to field a more likeable city. Perhaps we were supposed to dislike them before for not helping in the fight against Garlemand but that's poor justification in the light of the fact that they had been fighting their own war for centuries, in a land that had been recently rendered even more inhospitable by the Calamity-induced winter. Certainly, if the alliance wanted Ishgard's aid, I'd have thought it only fair they help Ishgard against the threat of Nidhogg's Hoard.
Anyways, since I liked the story enough, it helping there were fewer stupidly inane fetch quests (not Tataru's), I have decided to attempt to interpret what themes I can out of the main story.
So far, FFXIV in general has been about moving past tragic circumstances, like the Calamity and now the Dragonsong War, but Heavensward in particular to me, is about having one's beliefs challenged.
You can see this as early as the quests with Artoriel. He sends you off alone to deal with some heretics and partially hopes that's the last time he'll ever see you, a somewhat typical Ishgardian view of strangers. After you make it through though, he says what he had done and intended, explains that he was wrong, and then he apologizes and from then on was as far as I could tell, supportive. Actually, none of House Fortemps begrudges you for being the one Hauchefaunt died protecting, which actually hurt me inside somewhat.
Most of the good guys have a point in the story where they realize "Wow, I've/We've been doing something that seemed completely correct at the time, but is actually not so justified according to this new information." The big one is, of course, the origins of the Dragonsong War for Ishgard, but I love the choice of people who go to Dravinia because the three that accompanied you each had/have their own beliefs challenged.
Alphinaud and Ysayle are easy to explain. Alphinaud had his core shaken even before Heavensward, with his good intentions to make the Crystal Braves resulting in many perfectly good adventurers getting killed or injured. Ysayle gets a deeper grasp of the consequences of her fight against Ishgard, and learns that the dragons she fights on behalf of are not as noble as she determined. Estinien is an Ishgardian citizen and subject to learning about the truth of the war, but beyond that he managed to go from spitefully taking shots at Ysayle and threatening to kill dragons to respecting Ysayle and Hraesvelgr's brood (I think). Your comrades have what they thought to be true broken, and manage to adapt properly, and in the end affect good. (cont.)