So much to address... I'm going to bring this down to some main points you brought up since I can't possibly addresses it all, starting with...

Quote Originally Posted by Quite View Post
The first thing to rage about was being asked by Alphinaud what you thought on the Ala Mhigan rebellion. I was given three VAGUE options. I picked the one I thought was most in character with how I had answered questions in HW and ARR. And guess what? I get a 'sorry you feel that way' response. Not only did the response not fit any of the answers, I had now chosen a response that felt like I was playing Fallout 4. I didn't mean to say anything that implied what that response implied I said. The other times you choose words to say would mostly follow in that Fallout 4 'But I didn't want to say that!' feeling.
This is unfortunately true, as the WoL the things we get to say in reaction are terribly limited and don't often convey what we really want to say. However, you do have to remember that XIV's story is little more than an interactive book, while there is some flexability in things ultimately the story will play out in exactly the way SE wants to tell it which means they can't really give us "impactful" choices. On top of that, they have to code all of this in and they only have limited resources to do that, so they give us the best they can while still adhering to the previous limitation.

Quote Originally Posted by Quite View Post
Then facing Xenos for the first time. He takes you down without effort and one of the characters states how useless everything you went through before is. Your esteemed allies and practiced soldiers just lose to everyone, even the foot soldiers of Garlemald. Seriously, what's the deal? You're trying to reset the novice feel? Why? Why on earth would ANYONE do that in that way, after building us up that much, now we're nothing but helpless to ONE PERSON who is HUMAN and equipped in armor that isn't that different form people we've already defeated? That was the moment where I felt further from this game than I ever have. And quite frankly, it broke my suspension of disbelief. Everything that happened afterward failed to connect with me because I was constantly thinking, "The devs want it this way, it's gonna happen this way."
You're right, the Devs wanted it that way, they wanted a couple things actually:
1. They wanted us to look at Zenos and wonder what the heck he actually is.
2. They wanted to show that there is a LOT of things about the world and about the Echo (which is what makes us the WoL) that our characters, the Scions and ourselves don't know.
3. They wanted us to HATE Zenos, more than we've ever hated anyone before.

Quote Originally Posted by Quite View Post
Rhalgar's Reach, after 20 years of not being spotted, magically gets attacked. There is no reason for this. None. There was specific interest in quelling these rebels yet none of Xenos' men had located it despite trying. So tell me, how did they know? And don't give me that 'Fordola knew where it was' excuse. If she was blind enough to support the empire then she would have outed them years ago with the zeal she has. This is a plot hole, and it's the ONLY REASON we decide to head for Doma.
This is actually due to how Zenos is as a person. Simply put, he didn't view the resistance as a threat so he had no reason to worry about putting them down. Actually letting them carry on served his purpose because Zenos wanted one thing above all others: A worthy opponent that could make him feel -anything-. Zenos only was able to experience emotion when he was in the thick of battle, kill or be killed. He was a true psychopath and the WoL was the ideal person who could stand against him as a worthy opponent. Had there been no resistance in Ala Mhigo then it's entirely possible we would not have had a reason nor the ability to invade Ala Mhigo, and Zenos was not going to invade the rest of Eorzea as he was under orders from the Emperor not to do so. The only way for him to get the fight he wanted was to have us come to him, and the resistance served that purpose perfectly.

Quote Originally Posted by Quite View Post
The next disappointment is the Ruby Sea. Look, the underwater parts were amazing, but it felt smaller in scope than Sastasha. To be specific, the location of the entrance to the Ruby Toll was so close to Doma that an entire sea was shrunk down to the size of a river. It felt like a river. Not a sea, a river. I just don't understand. Why did the map have to include the shore to the mainland? It would have felt so much bigger if the Ruby Sea was treated like the various maps in the Sea of Clouds: One section of many others. A new second map wasn't needed, just the illusion that the part where map was was only a small section of a larger archipelago in the middle of the sea. Have an ocean view instead of the Doma shore.
I agree that this zone was technically smaller than it should have been, but I decided that this archipelago was the Westernmost portion of the sea and that entrance was just a boat ride between Kugane and the Ruby Toll.

Quote Originally Posted by Quite View Post
Now, until this point, a lot of my complaints could be a result of the development process not being completely in sync. However, Yotsuyu is completely on the writers. She had a legitimate reason to betray Doma, it's how she - an abused and tossed away girl - could make money and scrape out a living that was more dignified than that of a whore. She also developed a sadistic side. But no, the entire focus of her story was how all Domans deserved death and she spoke to her subordinates like she knew we were listening. That's meta (acting upon knowledge the character shouldn't have) and a poor excuse for giving her an air of mystery. I actually thought that she was born in Garlemald for how distant she seemed from "her people".
I think there's more to Yotsuyo's story that we don't know yet and will get in later story as we progress through the patches.

Quote Originally Posted by Quite View Post
And what about Yugiri tossing all her patience to move the plot forward? She has never been that excited about anything, not even finding her master. But suddenly throws all caution to the wind for the sake of plot when it comes to attacking Xenos. I can't help but feel that 'standing up to Xenos' scene could have been accomplished more effectively (and believably) by chasing that young kid in the orange attire after hearing that he is attempting an assassination of his own.
This was because Yugiri lost her patience with their people of Doma and she was dedicated to saving her master's life, even if it meant throwing away her own life. She doesn't want Hien to die, and she doesn't want him to die because the people don't have the courage to fight. Also, remember, that up until this point Yugiri hasn't had any real "skin in the game", as it were. She wasn't in her homeland before, but she is now so everything is much, much more personal here.

Quote Originally Posted by Quite View Post
Then we free the nation of Doma... but it really doesn't feel like it. The map is still just as quiet as when we got there. Anyway, back to Eorzea.
No arguments here.

Quote Originally Posted by Quite View Post
Where I genuinely don't care for the story anymore and just want to get it over with. My suspension of disbelief is gone, I'm expecting a disappointing conclusion, and just want to get to the EX trials.

The conclusion was actually fantastic, except everything that led up to it was less than the outcome. I wasn't fighting Xenos in the end, I was fighting a primal. So all that build up and hype, and now the final villain needs a boost to keep up with us? When did we get so strong? I can't tell because we didn't actually fight a ton of big monsters beforehand. We fought enemies that everyone knew we were better than and only pushed our capabilities twice before that. 2+2 suddenly equaled 103 and I missed how we got there. When did we add 99 to that?
We always turn the dial up to 11 like this... Nothing new here.

Quote Originally Posted by Quite View Post
And now it goes back to my initial issue. Remember that dialogue choice I talked about? I gave the vague answer that most sounded like: "What about the ascians? I'll fight in this war while nothing else comes up but we really should be putting effort into finding them. This may be a good cause, but we ultimately have bigger issues." This game lost sight of the original plot and tacked on a conversation with one ascian at the end. What happened to all the primals they were summoning to make things hard for us all throughout ARR and HW? Why is the entire base story of an official expansion I paid extra for nothing more than a sub-plot? The ascians literally did NOTHING but wait for the Emperor's scheme to take place in a success via failure conclusion.
Yoshida was very clear that this Expac is NOT about the Ascians (even though everything eventually comes down to Ascians... I'm not saying it was Ascians... But it was Ascians), but more about Garlemald and dismantling more of their influence.

That's about all I have here, I'm sorry you didn't enjoy the story, I found it quite enjoyable, but you really needed to understand the subtext and the character motivations in order to know WHY things happened the way they did. I hope you find things more enjoyable in the patches to come.