I agree with your assessment of the story as well.
I think Bungie jumped, feet first, into uncharted waters with this new franchise, story-wise. With the Halo & Marathon series, it was a lot easier because the stories for each of those games were based on the perspective of a single protagonist whose actions drove the main plot and narrative forward. The overall backstory was filled in through the novels, comics & supplemental materials as well as in-game lore. With Destiny, the plot & narrative were developed without a single protagonist, which immediately cuts it off from the Campbellian "Hero's Journey" that is typically at the heart of such stories. Add to that the fact that they continue to utilize other familiar literary devices and elements which rely on such Monomythic staples and you can easily see the jarring effects for yourself. Blending a shooter with an MMO & RPG is proving to be not only a technical challenge, but a literary one as well, because of the clash in styles applied to each. The shooter & RPG genres use a protagonist-driven story structure, whereas the MMO relies more on background, lore and narrative to draw the player into what is already going on.
When one also considers the fact that Bungie has crafted this story to play out over a 10-year period, unlike their previous games in which the story developed with each successive release, with background & history being fleshed out in the novels, etc, and you can see how they may have painted themselves into a corner. I doubt they envisioned a 10-year story arc when they first set to work on Halo: CE back in the '90s. I also doubt that, when the game was released in 2001, they already had envisioned the Chief, on ice, floating toward a mysterious Forerunner planet in the ass-end of the FUD.
With Destiny, they already had a story set up. Then they had to scrap huge chunks of it & start over. On top of that, they have to stretch it out over a 10-year release schedule. It's almost the exact opposite of how they usually operate, so there is a LOT of stumbling happening, & it's the story that has suffered. Hopefully they can get their act together with the first Comet and get the story on track. They've introduced a ton of PvP and PvE activities to keep people occupied until the next updates, but that won't carry them for 10 years. Eventually, they're going to have to get the narrative moving again if they want to retain players. Sorry for being long-winded.