Working my way through my newly-arrived EE2 now, and I've spotted a few curious additions that seem like they're in there entirely to be future plot hooks. The Lambs of Dalamud being possibly active with the Au Ra, as mentioned above, is one.

One thing which did surprise me was that there's a beastman Saint: Saint Tataroon, a Qiqirn, of the Sapience leveplate. So far he's the only beastman canonized.

Also the records of a missionary expedition that ended up adrift and cannibalizing each other is kind of grim, but also strangely quick, given everything happened in the course of 24 or so days. One would assume they'd be able to last at least a few months, just for a regular ship voyage.