I don't know, Square's been pretty good with keeping their story straight from what I've seen. The mess with Thancred was kind of out of left field until you think about how the events following it even happened. No, I think the really mess plot isn't the metaplot but rather Raubahn's during Heavensward. It felt like such an afterthought, like, "Wow, this is shaping up nicely... but I feel like we're forgetting something... oh shit, right, him... uh, guys, quick, write something up for Raubahn!"