It bugged me after 6.3 and it still bugs me now:

If the Twelve was a "system" created by Hydaelyn and they "never manifested before men," then how did Eorzeans know their true names and at least part of their background stories? Even if something happened around Mor Dhona during the 3rd astral era and some men accidentally witnessed the images of one or two gods, was it possible that they got to know the names of the Gods and their charges that accurately?
So who spread the messages of the gods to Eorzeans but not anyone else in the world? Was it Hydaelyn? If so why would she do that? Because she loved Eorzeans the best?
Also, if the Twleve was to maintain the running of the Source, then did Hydaelyn create similar systems for the shards? At least we didn't get any clue either in the First or in the 13th.