The easiest way to pull all this off would be to simply avoid the main storyline altogether and introduce all new elements specifically for this world story, everything from characters to city-states. This may seem like a tall order, but nobody's expecting them to double game content in a single update. Simply introducing one element at a time is more than enough; they already do so with each expansion.

The biggest hurdle for all this would be the way that the main storyline dialogue is performed like it is dealing with current events. I myself haven’t gone through my whole main quest line, but from what I’ve gathered and seen myself, it deals mainly with the Scions, Primals, and Garlean Empire, among other things. A simple solution might be introducing a secret society that is not directly dealt with in the main storyline or just introducing new regions where these conflicts have no major influence.