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Cayde is on Nessus to get a Vex teleporter. Why did he want that? He doesn’t know he’s going to need to use it in the fashion he does later in the story. Again, the reason for him running off can’t just be “so he has the teleporter for us to use later in the city”. It needs to make sense to us and the character.

Just a nitpick, I guess, but Cayde literally tells us he was getting the teleporter so he could use it to get to Ghaul's ship and kill him.

I agree with a lot of what you've put down here. But I want to add on to your Setups and Non-Payoffs section.

Not only are we setup for Ikora's death through her musings, but we're setup, in my opinion, for Ghaul's redemption.

Granted, there's not enough material in the story between Ghaul and Consul to highlight a redemptive or transitional arc for the character. But, I felt, that it very much started to set up for Consul to be the greater threat, a puppet-master behind the curtain. Ghaul wanted to be chosen, not take the Light. I thought maybe Ghaul would refuse Consul's plan, but Consul would usurp his power over the Red Legion, and try to "take care of" Ghaul, and perhaps Ghaul would fight back, and maybe sacrifice himself to protect the Traveler from having it's Light taken, as he is interested in being Chosen. (Though, in all of this, it was our character who was Chosen....) Plus, Ghaul is in a white get-up. It seemed so telegraphed to me. But I guess not. Just another lousy boss who was a lousy villain.

I largely agree! Although I'm more forgiving of the flaws, probably. I have some more explanations on the plot holes, though.

I think we find out Cayde is on Nessus because of Failsafe's signal, though we only encounter said signal in game after already getting there. It's just poorly done? Looking back you put this in the connective tissue part, so, yeah.

The thing with the Warmind was to analyze the Almighty; and once you find out Zavala's plan is doomed to fail, it gives Ikora more reason to come with you. I suppose I can easily see where one might think this didn't have enough connection with Ikora's arc, though I personally thought it worked just fine.

I think the tension of disabling the Almighty made more sense from the perspective of the characters than the player, because while Ikora guessed the Cabal wanted to take the Light, they didn't know that Gaul was obsessed with it. For all they knew, the Red Legion would be okay blowing up the Sun if they had to to stop the counterattack, even if it meant losing their shot at the Light. So I don't think it was bad storytelling, but it was not optimal, either, and your idea might have been the way to go.

Gaul was an interesting villain, really, and I actually like how philosophical he was. It maybe wasn't the best route, but that last scene with the Consul really vindicated the structure of how you're running around and doing things mostly ancillary to the Red Legion until the end stretch, for me. If anything, I would have liked to see more reflection and conversation, even without more action.

On another note, I guess this means we maybe have a better idea of the consequences of Destiny 1's campaign ending. Now that we know that the Traveler was purposefully dormant- we helped it to quietly recuperate, by eliminating the Wizards draining its Light, and also by getting rid of the Heart of Darkness in The Black Garden I guess? I still don't really get that part; it seems like it should have been more empowering the Darkness than weakening the Traveler, if anything. Was there more explanation of it in Grimoire cards I missed? (Man, I still have to read all of that, some time.)

(I balk at the "therefore/but" rule, but I balk at storytelling 'rules' in general, because blah blah subjectivity. I felt like mentioning this for completeness' sake but don't actually want to talk about it, because my argument is mainly esoteric and irrelevant to the spirit of storytelling guidelines.)

Setups an non-payoffs

Ikora wonders about being mortal. About whether she could actually fight and risk her life knowing it’s the last one left. An interesting moment for her character, and something she’d definitely be wresting with. The speaker then talks about how bravery means death through sacrifice. Okay. Bungie is setting it up so Ikora finds her bravery, and sacrifices herself to aid the player in the last stand against Gaul. A nice satisfying character arc right? She could even come back to life when the Traveler reawakens and sends out its light. That way you could have your cake and eat it too, without breaking any established rules of the narrative universe. But… that didn’t happen. Nothing becomes of the setup, and it ends up being all talk. If you are going to bring up these themes, and you really want to hammer them home then you have these themes resonate in the characters and be part of arcs. Like, this is the kind of thing that makes stories GREAT rather than just good. Bungie could have even gone farther and have Cayde learn to be a team player or something. Again, the setup was all there, but it was wasted!

This was the thing that upset me the most, because there was so much storytelling potential here that went completely unexplored.

The speaker then talks about how bravery means death through sacrifice. Okay. Bungie is setting it up so Ikora finds her bravery, and sacrifices herself to aid the player in the last stand against Gaul. A nice satisfying character arc right? She could even come back to life when the Traveler reawakens and sends out its light. That way you could have your cake and eat it too, without breaking any established rules of the narrative universe.

Ikora was, I feel, the biggest letdown in terms of character for this game, which is a bummer, because her story is set up as being the core of the crux in being able to simply revive, and it directly ties into Ghaul's conversation with the player "You're not brave; you've merely forgotten the fear of death".

And a lot of that has to do with the fact that no, storylines like this shouldn't let you have your cake and eat it to.

To explain, let's look at the brilliant storytelling of Avatar: The Last Airbender.

(Spoilers!)
Early on, we're introduced to the character of Iroh. He is an extremely peaceful and patient man, who lives in exile with his nephew Zuko (the emperor's son). There is a bit of a disconnect between his personality and who he is in the history of that world. He was an extremely respected military general (the Emperor's brother, no less), and he is feared in legend, but all we see is a friendly man who tries to instill positive virtues on his angry and violent nephew.

We find out that his son was a soldier who was killed before the series began, and this led to the downfall of Iroh's military career at a pivotal battle in the city of Ba Sing Se. It changes him, and has a permanent effect on his character; if he had made different choices, his son (who was clearly taking after his father) would still be alive.
This all comes to a head in the episode "Tales of Ba Sing Se", where Iroh is in the city once more, only instead of waging war, he spends the episode helping random people in the city as he makes his way to a hill, spreading positivity, and changing people's lives in ways big and small. At the end, we see where it all comes from emotionally:

It really puts into perspective why he is the way he is, and why he doesn't give up on trying to steer his nephew away from a life of war and violence. Because war and violence have consequences, and they lead to sacrifices that can't be undone. It's a strong theme brought up early and often, and it affects all of the characters throughout the show.

The way this lesson plays out for his nephew is one of the most outstanding character/story arcs ever written (in any media, seriously).

And then we look at The Legend of Korra, The Last Airbender's sequel series, which took a surprising step backwards during its first season.

Early on, a clear threat to Benders (people who can control one of four elements) is brought up. An enemy that can permanently take away their Bending (essentially the same as Ghaul having the power to take away our Light), destroying everything that they are (in the show, the characters see it as a fate worse than death, since many of them base their entire lives/livelihoods on Bending). It's terrifying, and when the main character, Korra, (the Avatar, the only person in the world who can Bend all four elements) comes close to losing her Bending, the show has some subtle-yet-deliberate rape undertones that go with it:

(Best I could find, sorry, but it drives the point home well, as the episode ends on that note, leaving the viewer to marinate on it.)

It establishes the power that the enemy has over everyone, and as the show goes on, more and more people have their bending taken away from them against their will, and so the threat grows. When the only surviving airbenders in the world are targeted, the biggest BAMF of the show, Lin Bei-Fong, chooses to sacrifice herself in order to protect them. It's a great scene, and for the uninitiated (and because it's fitting here), here's a video that shows who she is as a character, and how her sacrifice is handled, all to the tunes of Taylor Swift (you people make me sick):

And it ties well to the theme explored in the first show, because we and the characters have seen it play out with Iroh:

Again, the episode closes with that scene, driving the lesson home once again. It's fantastic writing.

By the time the show comes to a close, Korra has lost her Bending, so despite defeating the enemy, we have a bittersweet ending, because the war between them has cost so much, and so many people, like Lin, are left permanently damaged from it. The cost is too much for Korra, and the show implies that she is contemplating suicide (going so far as to flat-out state that she's at her lowest point). Had the show ended on this note, I would have ignored all of its smaller faults, and hailed it as a mature exploration of the themes set up in the previous show. It said something, and drove it into our hearts...

Unfortunately, that's not how it ended.

Another big part of the show was that the protagonist, Korra, had no real connection to the strong spiritual beliefs and identity that all Avatars before her, and because of it, she couldn't Airbend (Airbenders being the most spiritual of the bending cultures, since they're essentially Tibetan monks). Despite this being set up as the premise of the whole show, it was handled poorly throughout, and you pretty much completely forget about it throughout the final episodes. Except during the last couple of minutes of the show, where this happens out of nowhere:

Bam. Korra and everyone else gets their Bending back, at no cost, and without any consequences whatsoever, starting with Lin.
The show's writers got to have their cake, and eat it too.

Those last two minutes ruined it for me, because the setup was given so much payoff throughout, while giving even more payoff to Iroh's lessons in the first show.
When we first meet the similarly-named Ikora in Destiny 2, she's in a similar low point. She discusses the philosophical nature of sacrifice, courage, and immortality (as does the Speaker, a fellow Warlock who knows these things). And them, we get nothing.
The Speaker dies, sure, but Ikora is never seen to sacrifice. Faceless Guardians? Yeah, sure, they get their one second of screentime, but nobody addresses it. Hawthorne points out her and her peoples' mortality, but in the end, she's dubbed a "Guardian" too, and that's it. No, Guardian's aren't on the same level as people like Hawthorne. It's even pointed out that Zavala can't really grasp what it means to only have the one shot at life, and the ability for it to be snuffed out permanently by a single enemy bullet (and what it means for people like Hawthorne to rush into the fires anyway). Ikora claims to be terrified of it, but in the end, she does it without breaking a sweat, and mostly offscreen.
It doesn't sell the idea, it doesn't explore the concept, and ultimately, she's the weakest character. Sorry sensei, but you should have died. The Speaker faced torture and death without flinching. He explained his philosohy, and walked the walk to the bitter end. Ikora just felt sad for a few days, then went right back to business as usual...

So yeah, stuff like this has haunted me for a while...

tl;dr:

Blow up the ship, which is not a threat at all at this point in time.
Assault to take back the city.
Gault takes the light.
Final Showdown.

This bugged me too, but I assumed I was missing something.

The mission to destroy The Almighty tried to make it seem like the Sun was going supernova at any moment and we had to stop it. But with Gaul still on Earth and his entire army still in the solar system, surely the danger could not have been imminent.

But you destroy The Almighty and... it doesn't seem to matter much, least of all to Gaul. It's not like he was using it as leverage. The Almighty gets blown up and all that happens is Gaul's adviser mentions it in passing and the game continues as normal. The final showdown continues exactly as it would have if the Almighty had still been there, or if it never even existed.

Second: Can the light be taken or not? The speaker tells Gaul that the light can’t be taken; it can only be given. Then, in a mission on Io we check out an experiment which was trying to extract light and give it to other lifeforms. At the end of the mission we are told the experiment failed and that won’t work. Okay, so the game is telling us Gaul can’t take the light. But does this not completely nullify Gaul’s storyline? The traveler sure as shit isn’t going to give Gaul its light… so he’s failed before he’s even begun. But oops, I guess he can take it after all, as that’s what he does for the finale. So why on Earth would Bungie be setting up the rules of light such that they completely remove any drama or worry with regards to Gaul, and then go and just break that rule? Worse, it just makes all the scenes with the speaker pure wheel spinning where no plot propulsion is happening. We learn about him and his past, which is good, but no actions actually materialize from this that matter within the overall narrative.

All the talk of taking and giving light does seem like a lot of mumbo-jumbo, but are we sure what happens with Ghaul at the end of the game? He "takes" Light in that he is able to wield supers (which was spectacularly terrifying, btw), but he has definitely not become a Guardian, as his resurrection is not Ghost-driven and uh, short lived. Some Grimoire cards would be nice.

How would my guardian, or anyone for that matter know that’s where Cayde went? How did they find out this information?

Failsafe boasted his distress calls into space. She tells you so during the first mission on Nessus.

Cayde is on Nessus to get a Vex teleporter. Why did he want that?

To teleport right next to Gaul and shoot him. He tells you this directly.

On Io, we do something with a Warmind… which has no connection to anything. Maybe I just don’t remember, but how did anything we did on Io lead to Ikora coming back? Again, we lack the narrative / logical / emotional connections here.

We used the Warmind and it sensors throughout the system to find the Almighty which in turn convinced Ikora that dying was worth saving the solar system. It also gets us scans of the Almighty so we know how to kill it.

(Sorry for the delayed response. I’ve only now started my 2nd play through and am coming across the answers to your questions.)