We at least know Team Xen's plans have something to do with Storm-9 (the catastrophe who destroyed the region like 50 years ago). We also know they want in some way to get Melia or Melia's powers, and in turn we know that Melia is (or have been in another identity) the child of Indriad/Sirius (even though Venam doesn't recognize her nor her ghost mother) and was also taken by Stormchasers. And for the third part, we know Storm-9 had something to do with the plans Indriad had in the long play (Vivian's sacrifice hints thad she softened it but couldn't avoid it entirely. So we got it narrowed down to the triangle between Xen-Melia/Maria/Marianette-Indriad's catastrophe.
I also thing a lot of mysteries are for sidequests to resolve, but I think we are already able to infer some things.
Having said that, I also agree that, while is good to know how to set mysteries up, is also good to know how to solve them satisfactory (See: Lost, Fringe, etc)