Complete Monster: Commander Lyle Tiberius Rourke is a tomb-robbing mercenary (or, as he insists, "adventure capitalist") solely in the Atlantis operation for profit. The leader of the expedition sent to find Atlantis, Rourke maintains a gruff, militaristic indifference to the lives of those lost to the Leviathan and upon seeing the Heart of Atlantis, plans to confiscate it and sell it for double the money he'd receive. When told that taking the Heart of Atlantis will kill every Atlantean, Rourke proudly plans to triple the price for it. When Milo refuses to cooperate, Rourke threatens to shoot Princess Kida and shortly thereafter murders her father, never dropping his friendly façade. Rourke was concerned for little else but himself and the potential profit he could reap from Atlantis, to the point where he tosses Helga off a blimp to her death for a minor benefit to his escape, and was greedy enough in the end to make his entire party turn against him.
You could argue this was Disney's attempt at adapting the Stargate franchise.
Crazy Awesome: Gaetan Moliere. The man is completely obsessed with dirt... and it makes him incredibly useful. He's able to identify Milo as a linguist by Sherlock Scanning and tasting dirt from under Milo's fingernails.
Genius Bonus: They did some research and then deliberately played with it.
Ichthyologists and paleontologists in the audience had to laugh at Whitmore's aquarium, which contained coelacanths (a 65-million-year-old species that was thought long extinct until its rediscovery in 1938.) Probably meant to show, in the most obscure possible way, that Whitmire's been exploring the world long enough to find all sorts of hidden things.
Cookie shows off a map on his belly showing "all 38 states." There were 38 states from 1876 to 1889 (meaning he got the tattoo sometime between age 33 and 47.) He seems to think there are still only 38 states, but then, he's not all there.
While abandoning the main characters in Atlantis, Rourke mutters, "P. T. Barnum was right." Mere gibberish unless you know Barnum's most famous (and probably apocryphal) saying, There's a sucker born every minute.
Cookie is confused when he finds a can labelled "cilantro" in his supplies at the start of the mission. Cilantro — Spanish for coriander — was called "coriander leaves" until the 1920s (it was introduced to British colonies in North America in 1670).
Moral Event Horizon: Rourke crosses it and keeps on going when he punches the elderly King of Atlantis so hard it causes internal bleeding, eventually leading to his death. Dr. Sweet drops out without hesitation when he sees this happen 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. For some people, don't talk about it.
So Okay, It's Average: The general consensus seems to be that it has a lot of good points, but a lot of bad ones too with each kind of balancing the other out.
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.
Vanilla Protagonist: Milo's not exactly a Flat Character, but he's also not very interesting either (especially compared to the herd of quirky supporting characters). He's just a nice, normal nerd with a talent for linguistics who gets to go on an adventure.
Vindicated by History: The film was neither a huge financial or critical hit, and perhaps received one of the most lukewarm receptions of any Disney film at the time. Many questioned Disney on its choice to pursue an action-oriented animated film, one that was designed for an older audience in mind and resorted to the extensive use of CGI when traditional animation had begun to lose favor at Disney. However, these days it is becoming a significant cult classic with more and more viewers taking a closer look at the film's merits. Those who enjoy it tend to appreciate its comic book style animation and its many adventurous elements, while many in its supporting cast have grown to be fan favorites among some, especially Audrey, Kida and Vinny in particular.
Visual Effects of Awesome: The film has very good animation on the whole, but the animation on the Leviathan is amazing. Similarly, any scene with Kida and the Crystal is bound to have this.
Win Back the Crowd: This was Disney's attempt to achieve this with more adult audiences, with a heavier emphasis on action, philosophy and steampunk as prominent features of the story, complete with a Darker and Edgier tone. The end result however ultimately did not achieve this effect, and like The Black Cauldron before it it would be some years before Disney fans would come back to reevaluate its good points, eventually granting it new life as a Cult Classic.