The creators for Atlantis mention that they are 
Miyazaki fans. One of his most beloved works is 
Laputa. This was work that Gainaxx most heavily 
borrowed from when they made Nadia in my opinion.

In Laputa, a princess (who doesn't know it), is 
being chased for the glowing blue pendant by a 
group of air pirates. Eventually she winds with 
the boy who helped her to escape the pirates on a 
flying battle ship where they are chased by the 
bad guys and after a fight wind up escaping to 
Laputa. The ending is in the same vein as both 
Nadia and Atlantis (but I am not going to spoil 
the plot by releaving it). Gainaxx did introduce 
many of Jules Verne elments into Nadia which were 
not present in Laputa, but then again, they had to 
fill 39 eps rather than 100 minutes.

While the similarities in the character designs 
cannot be explained by this, this could easily be 
the reason for the plot line similarities.

Marcus