My theory behind the Hydaelyn disappearance is that she really isn't 'gone' but doesn't have enough strength to talk to us/help us as much as before, because we have effectively been draining her aether into Zodiark (the dark blue/purple crystal, Lahabrea mentions their deity (and we know that the crystals are deities, as Hydaelyn is one) is shattered (and we all know that crystals shatter). What's more is that all the attuning crystals for the elemental Primals are bluish/purple iirc, I found this odd at first because shouldn't Ifrit's crystal be red/orange since he is a fire Primal? Well what if those attuning crystals are actually shattered pieces of Zodiark himself? And by using them to summon Elemental Primals from the aether, it is functioning as a tool that is converting Hydaelyn's Aether (so to speak) into Zodiark's Aether (again so to speak), just as we have the Blade of Light that does the exact opposite. The only Primal whose crystal isn't that color is Odin's however if you have completed Urth's Font you learn that Odin--the person on the horse in particular--isn't really a Primal, and that it is the sword that is cursed and absorbing the Aether from the Shroud, not from any kind of crystal, Even Bahamut's heart in Coil is of that purplish color crystal.
So yeah that is my hypothesis on what is going on in terms of the Mother Crystal (Hydaelyn) and more than likely the Father Crystal (Zodiark).