These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Commander Lyle Tiberius Rourke is a tomb-robbing mercenary, or as he insists "adventure capitalist", who's Only in It for the Money, but what cements him is his attitude toward his current assignment. He takes the Heart of Atlantis, which is precisely what keeps the Atlanteans alive. Without it, they'll all die. Many other villains wouldn't be aware of this, and most would leave it once they learned that. Rourke, however, takes it knowing that the civilization will die, but his greed is so great that he doesn't even care. Later on, in order to ensure his escape, he throws his loyal Dragon off his ascending zeppelin, joking about it and capping it off with a "Nothing personal!" What's rather frightening is that it really WASN'T personal; he hadn't had any problems with Helga beforehand, and betrayed her simply because it slightly benefited him.
Genius Bonus: Pay attention to the fish in Whitmore's mansion. They're coelacanths, an ancient and mysterious "missing link"-esque creature...which were believed extinct until 1938. The movie's set in 1914. Presumably, Whitmore's just that awesome an explorer.
Moral Event Horizon: Rourke crosses it and keeps on going when he punches the physically weak elderly King of Atlantis so hard it causes internal bleeding. Dr. Sweet drops out without hesitation and while the other main crew members don't, Audrey and Vinny at least are shown to be disconcerted and repulsed.
Sequelitis: A running theme in the Disney Animated Canon, as this film does indeed have a sequel. The sequel consists of three poorly-animated episodes of an aborted TV show strung together into a nonexistent narrative. Don't talk about it.
Theiss Titillation Theory: Kida's Atlantean clothing bares much skin. Okay, so that's an Atlantean thing. Helga, on the other hand, wears some things with straps. Often, there is only one firmly on a shoulder at at time...
They Wasted a Perfectly Good Character: Lots of effort is devoted early on to establishing this huge herd of interesting supporting cast members, who then spend the rest of the movie tripping over each other for screen time to the point where it feels like all of them got shortchanged. If the proposed TV series had materialized (see "Sequelitis" above), they would have each finally gotten a chance to shine.