I was looking over the Ver. 2.0 announcements as well and thinking about the Dalamud Ramifications. So, here's my take:

1. Dalamud is successfully crashed into Eorzea, causing a period of darkness (say, 1 or 2 generations), and we time skip forward. This would explain how they said we may be able to re-make our characters (think sons or daughters of our current characters). The "Tree" things are actually shards of Dalamud that have been overrun by the flora of the planet.

2. Something causes Dalamud to be repelled, but also causes the Geological deformations in Eorzea. For this scenario, My guess would be that the Eikons band together to fight off the Dalamud meteor in some way, but linking it to the geological deformations is a bit tougher. Maybe some sort of Aether "cannon" (not literally) that is controlled by the Eikons in order to prevent Meteor.

3. Something else entirely, because you never know when it comes to plot twists! ^_^

...Honestly, I like scenario 1 the best. Dalamud crashes into Eorzea in fragments, the Empire "wins" but at a significant cost to themselves. Then we have the time skip, allowing people to re-imagine their characters utilizing the 2.0 game engine, and the time skip will also allow them to explain any changes to civilization (Gridania and the Black Shroud changing, etc.).
As for the OP alternate universe theory, it's interesting but unlikely given the devs have so much invested in the current lore of the 12, Eorzea, The Empire, and the Eikons.