Hi Emma
While I have the whole Nadia epic, I must confess that I haven't viewed it all - frankly I got bored with it. But I still feel that there are far too many similarities between it and Atlantis to be co-incidental.
Yes, the story you have described is far from Atlantis', but its also not that far removed in certain places. To claim the similarities exist because both take 20,000 Leagues Under the Sea as their inspiration is somewhat illogical, because as far as I know, no version of 20,000 Leagues under the Sea includes Atlantis, energy christals, no extinct/abondoned ancient civilisations at all infact. Nor does it include anybody wanting to take over the world (although Nemo is a terrorist who strikes out at the British Empire).
In fact, beyond the fantastic nature of Nemo's ship, 20,000 Leagues is not such a fantastical story - Two or three biologists are sent on an expedition to locate/identify/destroy a huge sea creature that is sinking ships. They end up stranded on the monster after an encounter in which the creature sinks their ship, only to find that the "creature" is in-fact man made, and Nemo's Nautilus. Nemo is an Indian who has removed himself from society, and attacks British shipping, because the British Empire were responsible for the deaths of his wife and children. The scientists are held prisoner - for Nemo fears if they are let go they will betray him to the British authorities. The majority of the novel involves non-exciting "routine" travellogues until the giant squid attack towards the end, and then the scientists manage to escape when the Nautilus gets caught in a whirlpool - the fate of Nemo and his ship is not revealed.
True, there's a couple (I think) of other Nemo books, at least one of which is a prequel (and involves ret-conning of Nemo's history and motivations if I recall correctly). I don't think either of these involves anything remotely like Atlantis (the place) in the story, or energy chrystals. Sadly I'm at my parents this week so can't check my
Encyclopedia of Fantastic Victoriana)
Nadia and Atlantis are too similar, far to similar and unlike their inspiration to simply claim this is where the similarites come from - you don't have to copy wholesale an idea or concept to plagorize it. Nadia lasts for hours! Atlantis is a movie less than two hours. Of course its going to be different.
Regardless of if Atlantis is or is not a deliberate copy, the fact remains it looks suspiciously like certain parts are. And after the Kimba/Lion King fisaco, Disney should of had checks and balances in place to stop them being placed in such a position again. I'm sure Disney aren't as forgiving when it comes to other films/books having similarities to their properties. It's not as if in a lot of cases where copying is accused, that this is from an unmade script.
Of course, the biggest case of Disney copying another concept/idea is The Incredibles.

When does homage end and copying begin?