I agree with most of this, I've still got some story to go, but I'm having to force myself through it; the only part I've really enjoyed so far was the episode on the Azim Steppe, which was all to short.
I also find myself rather resenting Lyse and Alisaie for their parts in the story. Lyse I could live with even though her backstory is pretty stupid, but (as my FC mates have heard a dozen times by now) just about everything Alisaie does makes me hate her just a bit more. I LIKE diplomacy, thank you, and while I could have respected her for wanting to take a different approach, I feel like she spends a lot of her screen-time putting down her brother, usually when he's not even around, in a pathetically transparent attempt by the writers to both pump her up as a character and curry favor with the small but loud section of the playerbase who dislike Alphinaud and found all the politics in Heavensward frustrating.
The breaking point for me was her suddenly screaming about how Alphinaud TOTALLY can't swim, but SHE swims like a fish, out of nowhere, several scenes removed from her brother's last appearance. It was extremely weird and tonally inappropriate, and really just made her seem like the sort of nasty person who makes mean jokes about people who aren't around to defend themselves. If he'd actually been around and she'd been doing it to directly tease him, it would have felt...almost like a cute sibling rivalry thing, with maybe a few shades of her being self-conscious and childishly trying to make herself look better to the rest of the group by putting him down. STILL not the most likable personality trait, but an understandable one.
I guess the writers REALLY wanted to make us like her, and somehow it never occurred to them that having a character we barely know constantly take pot-shots at one we've spent the better part of four years of story becoming attached to might actually hurt their case?
And that's not even touching on how out of character Yugiri was, or how she was barely around when this should have been their chance to flesh her out and give her enough screen time to justify all the love she gets. Or how Yotsuyu was written as a cackling, irredeemable villain right up until you defeat her and unlock a sudden infodump about her tragic past? It's just bad writing, and should have either been uncovered piece by piece well before you go to Doma castle, to give you an actual feeling of conflict in going up against this person who legitimately deserves your pity despite her evil actions, or left out of the MSQ entirely and made fodder for a sidestory.
But really, all the problems come down to the story being rushed. I'm not saying that SE rushed production or anything; the STORY itself rushed by trying to cover too many things in one great glut. We rushed through liberating TWO entire nations in just ten levels worth of story, so we ended up glossing over or speeding through a lot of things that should have been major turning points in the story. Liberating Doma felt anticlimactic, and even losing Gosetsu, the only character in 'your party' with a personality, barely warranted a pause to mourn him, and then you literally ditch the victory celebration to rush back to Eorzea, like it hasn't been fine without you for the past few months the Doman campaign would realistically have to take, and won't keep long enough for you to take ONE NIGHT to actually enjoy having accomplished something.
4.0 should have ended with Doma's liberation, and Ala Mhigo should have been saved for 4.1+; the game would have been much better for it.