Zodiark is technically just another Primal, 2.0 is meant to conclude the Primal threat storyline, so it's likely the Ascians/Zodiark will be dealt with by the end. They could always return though, I kind of get the feeling that Lahabrea is making his own plans...
That said, I doubt the Mystery Trial will be anything significant to the story, considering it is in 2.5 not 2.51+ where the story concludes... I find it far more likely it will be another Ultima Ballad style fight, perhaps with Gaius van Baelsar and his team of utter weaklings.
East, then to the past, then west, if Final Fantasy XI is anything to go off. Who's to say Zodiark is even the only dark god? They've got plenty they can do given XIVs fanservice nature.