There were three Atlantean Ark-Ships that made the journey to Earth. Episode 35 will reveal what became of the other two in the 2 million years since then.
Red Noah states Nadia is the true succeessor to the Blue Water. But how can that be if Emperor Neo rules? While it can be hand-waved initially by the Ship being not caught up on current events, it's another clue that Neo is effectively as good as 'dead' and only has custodianship of the Blue Water because Nadia hasn't embraced or rejected hers yet.
Genre Shift: This episode really begins the final Genre Shift of Nadia, as the Steampunk aesthetic is further phased out in favor of heavy Science-Fiction and seguing onto the cusp of Space Opera.
Hope Spot Again, a Meta example. It seems like the Filler episodes are finally over and the plot is getting back on track. Unfortunately, there are still 3 more filler episodes to go...
Sapient Ship: Red Noah has an automated robot pilot that slowly seeks the heirs to Tartessos to restart the Atlantean civilization. It used to be housed at Atlantis until the latter was decimated by war; it camouflaged itself as an island and ebbed for thousands of years until it stumbled upon Nadia while they were marooned on Lincoln Island.