What happened to Mara Sov and the awoken? What happened to Saladin and the Iron Temple? What happened to all the Siva stuff? What happened to the Cosmodrome, Moon, Mars, Venus and the dreadnought? Who was the Stranger? I did not expect answers this is just to track what was left unanswered. I don't expect them to be answered considering it is Bungie.
1) Mara Sov is currently MIA. I would think we'll see more of her when the next Fallen-focused expansion comes around, seeing as the Awoken and Eliksni seem to be closest of any two races. 2) The Temple itself likely is unsafe, seeing as Tyra Karn is currently residing at the Farm in the EDZ. As to Saladin...it's possible he didn't make it out. 3) SIVA (a) is currently inert/destroyed by our hands, buried under the wreckage of the bunker. However, there are other samples, such as SIVA (b) which is somewhere near the Exodus Black. 4) The original areas are, at the present time, non-significant to the Red War arc. Presumably, they've been occupied, but don't hold any real importance to the Cabal. 4a) The Dreadnought is likely considered too much of a hotzone, and is simply being ignored, for fear of the Taken 5) The Stranger is still a mystery. We may find out more, if there's a Vex-focused Expansion