Bungie seems to have forgotten about a ton of things in the game, to be honest. Let's run through a list:
-Osiris. Where he at?
-Exo Stranger. Remember her? You don't, because no one mentioned her since before Dark Below. And you stopped replaying old missions during House of Wolves.
-What's up with the Exos in general?
-Where did Mara Sov go? (To be fair, this one is rather recent)
-Why was the Festival of the Lost such a non-sequitur?
-What about the weird artefact the Awoken have?
-What about the weird artefact Dead Orbit has?
-What about the weird artefact that Future War Cult has that lets people see the future?
-Why, after two years, is a third of the Birth of History still missing? Where did it go?
-What's up with the Vex? Who built them?
-Seriously, how did no one notice billion year old ruins on Venus?
-What do the Cabal want? Why are they here?
-You remember that Traveller thing? You know, the giant orb on the box art and all the promotional material? You remember it, right? Cause Bungie sure doesn't.
-Wouldn't it be so cool to see an Ahamkara?
-The mother effing box of planets in the Grimoire. Seriously, what the actual eff?
-Why does no one want to acknowledge the fact that my Ghost went through reverse robot puberty? Is this an effect of my fight with Atheon?
Feel free to propose more mysteries and unanswered questions.
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If I am correct the original story writer left. This means they had gaps in the vanilla storyline and it's obvious to most people to what happened. Trust me the story is going to be better for Destiny two now that they had their new writer have time to finish it up.
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Good questions, but also consider it is only y2 of a 10 year franchise, they aren't going to expose everything right away.