I've finally caught up with this awesome AAR, so now I have to wait for updates. Sigh.
I really enjoy the concept, and not just because it's different than the usual AAR. Simply as a story, I'm really enjoying it, although I have no idea how you're going to explain the shift in timelines in 1533. Perhaps the detonation of the Water Dragon opened a subspace fissure in the transdimensional planar field allowing a cascade failure of ionized quantum tachyons, which defribillated the temporal strands, causing them to reset to their base settings. Yeah, I watched too much Star Trek as a kid.
My favorite part was the Byzantine section, partly because Byzantium is my favorite EU3 country, and because it was epic. It did a good job of showing the epic last stand of a once glorious empire, now stripped of all her majesty but determined for one last time to make the nations tremble.
I'm looking forward to the Incas. But I do hope that Talena still honors the memory of Zoe, even if she no longer existed, and one day restores her empire to glory.