I always thought it would have been nice if Cid got trapped in the World of Darkness, saving Nero, effectively having Nero fill his role for a time. Though the developers utter reluctance to tie past content together (meaning Crystal Tower could never have been a requirement for Heavensward, despite Heavensward being just as unfriendly to get into to new players anyway) means that could never have happened... How good would that have been though? Not to mention how perfectly it ties back into the Void Ark content (I'm still hoping Nero is the leader of the Sky Pirates for reasons, and his whole motivation is given depth with the completion of World of Darkness (researching the Void to save the clones), plus Sky Pirate Nero might as well be Balthier, and being Balthier is the only true way to beat Cid). The fact that all pieces of content are effectively their own little instances, with no overlap because we can't make things like Crystal Tower a requirement for anything (again, despite making all of 2.x a requirement for Heavensward...) is a large part of why this games story lacks depth IMO, and a reason why I consider stuff like Hildibrand and the Mail Mog stuff to be better than certainly 2.0... I mean, Final Coil spoilers;
When Louisoix is Phoenix... I know he said not to summon him, but had Final Coil been a requirement for for Heavensward, we could have had a much more satisfying resolution to the Ul'dah plot... "Oh, Nanamo is dead? Screw it lets summon Phoenix", "Oh, the Scions are dead? Well we need them, hey Phoenix?!", both more satisfying than the "Gotcha!"'s being pulled for those points... Heck, don't even need to summon Phoenix, have the old bird have gifted them with OP Phoenix Downs at the end of Final Coil... Don't even need to have completed Coil for that to then work, it can just be another case of what I hope they do with Nero/Void Ark, where people who've done Coil can go "They're using the thing from Coil!" and people who haven't can go "Where'd they get that?" and then do Coil and go "Ohhhh!". I wrote a better plot conclusion in a rant SE, dwell on that for a while, would ya?
As for Alexander... That story completely falls flat because it has absolutely no foreshadowing (that I recall, the Illuminati seemed more likely to summon a Cheese Primal before they randomly summoned Alexander...). Coils worked because right from the start of the game, you had an understanding of that plot; Bahamut showed up, wreaked the world, then something happened. None of the characters were randomly inserted like Mide is (though you'd need to have played 1.23 to really get the two main players in Coil, but they're still mentioned in the opening cutscene of the game). All of Coil is basically discovering the truth behind events presented to you in the games trailer. Alexander doesn't have that. He doesn't have anything. Everything related to Alexander is just plugged in at the end. "What happened to Bahamut?" was a question I was asking when 1.0 went down. "What is the Enigma Codex?" is a question I'm no where near as invested in.
You know what would have improved Alexander? Two things; One, make him a threat. Place some settlement off the map for him to have Holy Judgement'd when he was summoned, and have the gap between that and our Raid be him recharging. Bam, now he is a threat, though still no where close to "I had a whole trailer dedicated to me blowing up the world" level Bahamut and Coil got. Two, introduce Mide earlier, or if not Mide, the person she's looking for, or a friend of hers, or whatever. We had quests in Idyllshire. We could have had an NPC who had something (another piece of the Enigma Codex) guide us around through much of those quests. Come the end of those quests, the Illuminati could have killed him off, with some vague foreshadowing that they can't have the thing they took (the piece of the Enigma Codex). Then when Alexander rolls out and Mide is introduced, along with the Enigma Codex, all the pieces fall in place, and we're invested because of those early quests.
That would have been much better than "Oh hi, I'm Alexander, I'm going to spend the next year crawling out of this river, but please consider me to be a real threat". Bahamut was a real threat, seeing pieces of him throughout Coil made the Raid compelling just from looking at it. Alexander is retarded, and I mean that in the truest sense of the word; He is slow. He is crawling out of a river slowly. He hasn't harmed a single person. Heck the Illuminati haven't either really (during one of the quests they upset that one Goblin I think? Happened off screen though, of course). I might be interested in who Mide keeps talking about, but all my interactions with Mide are over, they were over very quickly. Meanwhile, Bahamut, Louisoix, Nael van Darnus, I got all of them years ago, long before I walked into the Binding Coil... That's why Coil had me invested, and Alexander just doesn't, never mind the fact that story mode effectively makes the true reward meaningless (at least IMO). I didn't do Coil for the gear, I did it for the story, and the challenge made that far more rewarding. That's gone with Alexander though.
As for that point... Yeah, Story Mode ruins Alexander. That's not to say I'm against it, I'm just against it coming first. When I did A1, do you know what I did? I predicted every change they made for A1S. "I bet we'll have four bombs, since there are four adds", "I bet that green AoE will stay there for a while like T1", "I bet they'll drop down differently, making the green AoE placement matter", you know what that did? It made A1S easier. Of course it did, how could it not? Even if you don't try to predict the changes, you're going to have a general sense of what to do than if you'd gone in blind, and you can't go in blind because Story Mode is a requirement... I'd have much rather seen Savage introduced first, with the Story Mode effectively being the Minstrel's Ballad; The Minstrel hears the tale of someone (not you!) clearing Alexander, and lets you recount the tale with the story mode. Perhaps tie it into server first, so a group on your server clears A4S, concluding the current Raid, then everyone can go unlock the Story Mode from the Minstrel, perhaps throw some recognition to the server first group with the quest? That's just a much more compelling system to me. It adds an extra reward to being server first (an actual reward rather, since world first is all anyone cares about). It doesn't force people who want the story to do the hard content, and likewise it doesn't force people who want a challenging story to do the faceroll content.
EDIT: Thinking about it, the best way to establish Alexander as an actual problem? Tiamat told us about Bahamut. Nidhogg got away. Have Nidhogg summon Bahamut in an attempt to destroy Ishgard, then have Alexander pop up and end Bahamut. Why does that work, other than it establishing Alexander as stronger than Bahamut? It works because it is a reference to the best Final Fantasy. Now that would have gotten me significantly pumped up, ready to be disappointed by the actual Raid.
You know what, screw it, just rewatching that got me pumped, that's my new head canon. Nidhogg was getting ready to attack Ishgard, summoned Bahamut, then Gobbie Justice got in the way giving us that epicness. No "Alexander is going to crawl out of the river". None of that, he is out of the river and recharging and everyone is terrified having just watched him prevent a second Bahamut flavoured Calamity. I didn't even really write this, Hironobu Sakaguchi did, well over 15 years ago. Who knows, maybe this can still happen come 3.4, when Alexander will finally have pulled himself out of the damned river...