Story Elements that need to be added or improved:

[Fendred]

I do not intend this to be a complete list of all things I found to be an issue in the overall story or setting, and I'm hoping others will add their observations to the thread to help build up the list. By the way, THIS THREAD CONTAINS SPOILERS FOR THE STORY! DO NOT READ BEYOND THIS POINT IF YOU DON'T WANT KEY STORY ELEMENTS REVEALED TO YOU! So, to start...

1) Baelsar teaming up with an Ascian: There is a difference between being "blinded by ambition" and being plain stupid. The story has depicted making deals with ascians as a surefire way to get screwed over. It would have made more sense if the ascian lord possessing Thancred posed as a traitor to the Seventh Dawn that was willing to give the Empire the means to conquer Eorzea under the pretense of solving the primals issue. This story issue could be solved, but Baelsar must of had some pretense to believe his dealings with an Ascian lord would not backfire and destroy his ambitions. As of right now, there is none.

2) Relationship between adventurer and Alphinaud not properly depicted: There simply isn't any events in the main story that would justify the trust our main character begins to show towards Alphinaud. One second he is a stranger, and the next we are buddy-buddy with him for apparently no reason. Not much can be done to resolve this, since it would mean including new cutscenes or dialogue along the main story arc which is considered finished.

3) Relationship between Alphinaud and Cid: Somewhat connected to number two is the relationship between Cid and Alphinaud. I'm supposed to accept that they're close enough to one another that Cid would be comfortable with Alphinaud touching him physically when the story doesn't even show any of this development? Because none of the development in their relationship is shown, nor any past experiences they've had together, the moment Alphinaud touches Cid's hand in a show of comfort/friendship (I guess?) just feels awkward. This could at least be explained away with some additional cutscenes in future patches involving the two characters.

4) The Thousand Maws of Totorak: A dungeon containing mutant plants and giant spiders is just a short walk from a nearby settlement, and the entrance to the dungeon is guarded by just one wood wailer? Not only that, but the wood wailer was not competent enough to spot a sylph entering a dungeon when the entrance behind him is the only way into or out of the place. First, why would anyone live near such a place, and if the place were not always this dangerous, why haven't the residents called in for aid from Gridania, if not for an entire army of adventurers to clean house? If that giant spider decided to burst through the doors of Totorak to attack the town for food, does anyone honestly think a single wood wailer is going to be able to protect the town? The best solution I could think of would be to have the seed seer place a garrison outside the place at the very least.

5) Why did the moogles accept a strange gift from a masked man that looks nothing like a wood wailer and projects a dark, menacing aura to summon their king, Moggle Mog? I never imagined the moogles to be this stupid, and I kind of expected they'd be able to tell the difference between a common wood wailer and a complete stranger, given they have lived in the woods for ages.

6) Why do the beastmen tribes trust the ascians enough to accept strange gifts from them? They inhabit human bodies, which gives them the appearance of their mortal enemy, and they give off a dark and menacing aura. From what I know about ascians, the beastmen should be killing them on sight.

7-8) Beastmen and Primals non-sense: Ok, so the Amal'jaa believe that all of Thanalan is their property by divine right. They summon ifrit in the hopes of conquering Thanalan. However, the primals temper all their worshippers, and when you are tempered, your previous objectives go out the window in favor of fueling your primal's power by getting him more worshippers. So summoning a primal does not actually complete their objective of claiming Thanalan for the Amal'jaa. Instead, it becomes about claiming all of civilization for Ifrit. They also have no control over Ifrit, so Ifrit isn't even a good weapon. He is a weapon that takes control of his users to achieve his own objectives. By the way, he eats the life force of his followers, so the Amal'jaa should expect a shorter life expectancy as well. The Ixali have a similar issue, where their objective is to gain wings again to fly, yet once tempered, they will only ever serve Garuda. Why aren't the beast tribes more visibly in a state of civil unrest with themselves? What happened to all the non-tempered beastmen who can see the obvious fact that these incarnations of their deities are no good? Yes, I know about the Amal'jaa warrior tribe in 2.1 and the good sylph. The problem is that there really should be a lot more of them, considering you have to be in the presence of the primal to be tempered, and there is no way opposing beastmen are going to just sit there waiting to be tempered. I guess I just expected to see more communication between the beastmen and the city states than what is present in this game. The current situation feels rather forced and unrealistic.

9) Binding Coil of Bahamut and the Echo: So we are plumbing the depths of an ancient Allagan structure rich in history, and our echo power doesn't even go off once. Besides raising an eyebrow as to how the echo works, it is also a genuine let down in the story telling department. As the player descends further and further into the bowls of the earth to whatever lies at the heart of the structure, wouldn't it be interesting if we actually got some lore on the Allagan empire itself and its reasons for disappearing? But it never happens, even though I positively love everything about the dungeon. I really would have liked going deeper into the structure to be like a journey back through time as the player's echo continues to show him more of the past behind the Binding Coil of Bahamut.

[Skies]

The part about the beastmen and primals, the 7-8 one, is actually quite sensible
They did not know at all what the primals would do with them, they were fooled. They summoned their primal with one intent, and then their primal takes them over. And then ones tempered go and temper others, which in turn temper even more of them, creating a huge snowball. The Beastman daily quests are, more or less, looking into the split between the few non-tempered ones versus the army of tempered beastmen.
You also probably don't know but in 1.x is where communication between city-states and beastmen fell apart. Trying to forestall the garlean invasion the city-states broke all relationship with the beastmen, at least the ones who summon, because the garleans made it clear they hated primals above everything, they thought that'd might make the garleans warm up to them as allies rather than lands to be conquered.
Didn't quite work, and left deep scars.

[WellFooled]

Its clear you've put a lot of thought into all of this!

In regard point 4, if I remember right the giant diremite you described is just a little tiny mite until the ascians somehow gives it super powers, so its a non-existant threat so far as anyone outside is concerned. The dungeon is always locked down with very sturdy looking doors to keep whatever dangers may be inside (mostly pretty average monsters really). It seems as reasonable a threat to live by as those that exist in all other areas of Eorzea. Also Slyphs can fly (and without making much noise doing it!), giving them an advantage in sneaking past guards :P

[NoloeTazier]

I was actually pretty disappointed with Gaius van Baelsar's story. In 1.0 he was a very smart, very proud, plotting man. He was always behind the scenes and pretty much knew what Van Darnus was doing but wanted to see how he and we Adventurer's responded. He was more than content to sit in Ala Mhigo (his arm atleast, ignoring his own personal sojourns into the realm) and wait things out. After all his duty was to conquer the whole of Eorzea, sit back and watch as Van Darnus' madness consumes himself, his soldiers, and Eorzea and then Van Baelsar could mop things up afterwards. After all Van Darnus' 7th Legion was made up entirely of brainwashed Ala Mhigans, not real Garlean soldiers so if they were killed it was just the Eorzean Alliance killing a bunch of Ala Mhigans. Now in the time of 2.0 Van Baelsar is ready to bring in the big dog to stop both the Eorzean Alliance and the Primals. The Adventurers were after all missing for 5 years, the ones who stopped Van Darnus' madness but not in time to stop Dalamud's descent (probably had more to do with gravity of the planet pulling it than the Lunar Transmitter itself which did indeed pull it, but we blew it up so in a way we failed that too). No one was left in Eorzea with power...Gais van Baelsar just spent his time making more Garlean strongholds but not really attacking the Eorzean people, sure a huge 'castle' like structure is intimidating but c'mon. In 1.0 airships flew above the zones of Eorzea, now that felt ominous, like any moment they could start firing or dropping troops..no fear of the Eorzean Alliance. Anyways I'm mostly rambling and ranting.

Van Baelsar just didn't come off as threatening to me as Van Darnus did. Van Darnus felt like a true villain, someone who does indeed wish death and destruction on Eorzea so the Garleans could take over. Van Baelsar felt more like "ok c'mon guys I have an Ultima Weapon, just kneel to us." Ultima Weapon gained power through the Primals and was able to FLY, we're on an airship and he didn't even wish to attack us or the cities. It became a "alright see you guys later in my dungeon." Which it became. No real threat at all, I'd have been fine if Nero wanted to gauge the new power of Ultima through tests at the Praetorium..but just flying off. It wasn't really thrilling to me, felt like a 50's horror. We were able to just fly away on the airship as Van Baelsar had finally unleashed his weapon, just to return it to base where it awaits us in a dungeon. Nice way of conquering Eorzea there. Yes I know people may say he simply wanted Eorzea to bend the knee and not wish too much bloodshed, after all what's the point of ruling someone if everyone is dead, but to me Nero was WAY more fascinating than Van Baelsar. Livia was more of a threat, Rihtahtyn was really a non-factor who should have been way more involved. A Roegadyn Tribuni to me just screamed for an in depth story. Van Baelsar just didn't come off as the main guy, sure the storyline had evolved from the Garlean threat into the Ascian...but Van Baelsar was a proud Garlean. He killed 13 men who sought to kill/steal power from Emperor Solus and I just still don't see him taking help from the Ascians' Lahabrea to use Ultima Weapon, maybe I could see Nero using the Ascians' to try and bump his reputation above Cid's and garner recognition for Ultima Weapon. Comes off as a bit rushed to me, merging the Ascian threat into the Garlean was bound to happen but the way it did just makes me "meh."

The Thousand Maws of Totorak had already been invaded by Garleans during 1.0, they had set up magitek devices for aetherial readings..the devices are still there lol. I believe they had 4 Wood Wailers standing outside it..but yeah most dungeons now just have 1. Doesn't really feel like anyone is guarding, more so just a NPC for people to talk to spawn the blue-glowy-enter-the-dungeon-thingy.

As for the Moogles and Beastmen accepting the "gift" of Primal summoning from the Ascians...well they weren't Ascians in 1.0. The Paragons were the ones who taught them (which we now know the Paragons ARE Ascians) but the Ascians we did see in 1.0 were Grim Reaper like and scared the Sylphs and Beast tribes greatly. Now the Ascians we know have hyur/human appearances. Maybe the Paragons simply were hooded men, the Beast Tribes were known to trade with merchants mostly with crystals, so a hooded hyur/human-esque person would not have appeared menacing to them compared to the GrimReaper like Ascian.

As for the Beast Tribes and worshiping the Primals, we do know that the Ixali worshiped Garuda LONG before they were able to summon her. It's religion, it makes people do crazy things. If the Amalj'aa and Kobold have similar histories with their Primals (a.k.a. worshiping them long before being able to summon) then I'd say it's just passed down through the generations and that you have ones who believe it 110% and you have those (The Ash Amalj'aa for example) who go against it, not wanting to rely on a deity they may or may not believe in (even though Ifrit clearly exists). It's not about wanting to control the Primal, it's their god, it controls them. The Amlj'aa first summoned Ifrit at Mythril Pit T-3 for the first time, many Ul'dahns were killed. We'll learn more about the Beast Tribes when we're finally able to access their home lands (Paglathan for Amlj'aa, Xelphatol for Ixali, and MT O'Ghomoro for Kobolds).

As for the Echo and the Binding Coil of Bahamut, we need someone with memories to be able to use the Echo and see said memories. Sure the structure itself seems active but if there's no memories we cannot Echo jump. It may also have something to do with the aether (memories and aether being a theory of mine as to why we were forgotten, Louisoix's spell altering the aether which affect everyone's memories of us, then we come back and people start remembering).

[Orophin]

Just to touch on Point #4, Sylphs can make themselves invisible so that's how it would be able to sneak past the guard. This isn't common knowledge though; something only 1.0 players would probably know.

I agree with a couple of your other points though.

Gaius's story and his supporting cast (sans Nero) had pretty weak character development.

The relationship between the player's character and Alphinaud, and Cid and Alphinaud felt pretty rushed.

Noloe summarized most of your later points up fairly well I think.

[Enkidoh]

5) Why did the moogles accept a strange gift from a masked man that looks nothing like a wood wailer and projects a dark, menacing aura to summon their king, Moggle Mog? I never imagined the moogles to be this stupid, and I kind of expected they'd be able to tell the difference between a common wood wailer and a complete stranger, given they have lived in the woods for ages.

6) Why do the beastmen tribes trust the ascians enough to accept strange gifts from them? They inhabit human bodies, which gives them the appearance of their mortal enemy, and they give off a dark and menacing aura. From what I know about ascians, the beastmen should be killing them on sight

Adding to what Noloe already mentioned, 1.0 clearly stated that the beastmen have a myth about the Paragons (told to the player by the sylphs), that in times of trouble the Paragons would appear and 'lead them to the wisdom of the Primals'. It's not too hard of a stretch therefore to see that the Ascians calling on the beastmen would have been taken by most of the beast tribes as their saviours, with obvious results.

Much of the Path of the Twelve storyline involved the player and their Path Companion going on an (ultimately unresolved) investigation into the Paragons because of this - they figured if they could find a Paragon there was a possibility that they could convince them to influence the beast tribes into laying down their arms. Of course in hindsight this seems somewhat naive, but as Noloe mentioned, the Paragon/Ascian connection wasn't actually known at that stage.

It's also stated repeatedly in ARR that the Ascians are experts at manipulation, that they prey on the weak minded and vulnerable, promising power and knowledge to those who feel put upon or powerless - the SMN Job quest line actually features this as a major plotline in particular.

[Wadoka]

...but you forgot the TRULY important unanswered question.

What about Aldis and Mylla? Where's the rest of *their* story? What happens after Highbridge?

[Enkidoh]

Aldis just went off on his voyage of discovery again, and Mylla went back to running the Colosseum like she was before. I thought that was pretty obvious and didn't need any further plot explanation in the game.

[Wadoka]

Aldis just went off on his voyage of discovery again, and Mylla went back to running the Colosseum like she was before. I thought that was pretty obvious and didn't need any further plot explanation in the game.

Have you no romance in your soul? That's extremely unsatisfying, a violation of Narrative Causality!

[Alberel]

Have you no romance in your soul? That's extremely unsatisfying, a violation of Narrative Causality!

Most of the class quest lines are left quite open after their 'conclusion' at 30. I assumed this was deliberate so they could continue them later.