Bungie already has a history of abandoning previous content. We left behind Year One guns and armors when TTK dropped. Thankfully those returned to us, though at a much later date and largely because Bungie needed to fill a space before Destiny 2 that would largely be considered a content drought for a looter-shooter like Destiny otherwise. Now, MAYBE their plan is to pretend some of the previous lore is going away forever and then bring it back later with the rest. Maybe they're trying to trick us into thinking it's gone, then bring it back to thunderous applause (which wouldn't happen, because we'd be too angry with them). Or maybe their plan was to test the waters and see how fans would react if they left the Exo Stranger behind, sort of check if they really need to fulfill that obligation or if they can scrap that particular story. And seeing our reaction, they'll know they have to tell her story. But for now, we have to take them at their word for this. And if their word is that they're leaving behind The Exo Stranger forever, and possibly others they haven't mentioned, then how do we know they won't do it again? Bungie, if you leave that thread unravelled, with large questions unanswered (like who she is, where she came from, why she thinks we're important, why the gun is important, her relationship to the vex, how she gets around without a ghost, why she's suspicious of the city, etc.), how can we trust you not to abandon lore, or other important content, again? How do we know you won't take us to year 6, decide that one of the coolest threads from THOSE three years isn't actually working the way you want, and then scrap that too by handing us a gun but no answers? Really, the answer is, we can't trust you. And earning back people's trust? Not an easy task.
Now, they never said FOREVER. ANYWHERE. They've said that some of those arcs are, in fact, sidelined for now because they aren't relevant to the current main focus. Which is Ghaul and his Legion. So, the Stranger (Staunch enemy of the Vex), Mara Sov (Possibly related to the Taken/Darkness), and the like are being pushed onto a shelf. Think of D1 as a pilot episode. Got a lot of info on the premises (What the races are, what the state of the world is, etc). From now on, we're getting the meat and potatoes of various stories. Cabal for certain in D2V. Maybe we'll get more on Rasputin and Osiris in the first two DLCs.