In regards to criticism claiming this movie's plot is too simplistic:

Frequent criticism of the film that I see on here and in other reviews is that it's plot is a rather straightforward action movie plot. I can't blame them, as the producers really never discussed the undertones of the movie.

I however noticed a subtle but very well done underlying message exploring man's responsibility over great power (and more specifically nuclear technology). For example, the opening scene of Atlantis falling prey to a tidal wave starts with a flash of light, a shockwave, and a great ball of energy rising into the sky in a mushroom cloud fashion (http://imgur.com/ECmCOWA). The King of Atlantis later explains that the disaster had not been a natural one as the Atlantian civilians were led to believe, but one of his own making:

"[...] In my arrogance, I sought to use [the crystal] as a weapon of war, but it's power proved too great to control. It overwhelmed us, and led to our destruction."

Evidently at the beginning of the movie Atlantis is enjoying a time of great prosperity, and has turned to finding the various ways the energy of the crystal could be used. The King had harnessed the power of the crystal in some sort of superweapon that the convoy in the opening scene deployed against an enemy city-state/civilization, but failed to predict the tsunami created by the resulting massive earthquakes.

The Atlantian king is horrified by his mistake, and in an effort to prevent it from reoccurring, seals away the crystal, disabling all of the technology powered by it. This parallels the longrunning debate against nuclear power. However, the film implies his choice may have been overzealous, and that moderate and responsible use of the crystal's power is possible. This is what makes the message well done; the film considers all sides of the discussion, rather than just having a "Nuclear bad" message. It's surprisingly three dimensional for a Disney movie.

Historically the film even references the secretiveness of nuclear technology and the efforts of the Germans to obtain it first (Milo: "[...] not to mention personally delivering the most powerful force known to man into the hands of a mercenary nutcase who's probably going to sell it to the Kaiser!").

Overall the film did an amazing job balancing a message with entertainment. The pace was absolutely perfect for both adults and children, but still managed to stop and carefully deliver such messages in a way that children will unconsciously absorb and adults enjoy pondering.