So, with no further ado, the reasons:
1. Joss Whedon worked on the story. That would be Joss Whedon, of Buffy, Firefly, and Avengers fame. He worked on the story. Which may be why the film kind of resembles an animated, underground Firefly. All the Whedon trademarks are there: the brilliant writing, the fantastic ensemble cast, the thrilling heroics...and the somewhat convoluted plot, though this one isn't as bad, probably because it's really a kid's movie.
The Shepherd's Journal from Atlantis
Shepherd Book from Firefly
Get it? Shepherd book?
(I am far too amused by this)
2. The movie is a overflowing fountain of nerd joy. Yes, beyond the Whedon connection. The linguist who developed the Atlantean language in the movie also invented Klingon and Vulcan. Leonard Nimoy is the voice of the king of Atlantis. Although I personally have not seen this movie, I have been told Atlantis shares some plot points with Stargate. I'll leave that to my readers to verify.
3. It, along with Disney's Treasure Planet, is steampunk. Well-done steampunk, with all the awesome that comes with it. Great big machines, subterranean landscapes with monsters and enormous sculptures, adventure, exploration, a culture with a language and customs at the center of the earth...everything Jules Verne-approved for maximum wish fulfillment. The story's style mimics the popular stories of the time the movie is set in (1914), which is kind of awesome, if you think about it.
4. For a Disney movie, it gets dark. It deals with some serious matter, like loss of culture and genocide (you know, for kids!). This adds matter to the story, which causes real thought and real feelings about the story and characters. This movie also is not afraid to kill characters off (see reason #1, above).
5. My favorite reason: Milo Thatch is basically, as my roommate put it, "skinny Steve" from Captain America. Let me explain. The moment in Captain America where Steve Rogers jumps on the dummy grenade as every other soldier runs for cover is the moment when you see that the reason Rogers is a hero has nothing to do with physical strength and combat ability. Here's the scene, below:
What's impressive about Milo in Atlantis is that he, too, is a hero for reasons beyond the physical. Atlantis goes further than Captain America, though, as Milo never gets good at fighting. Even at the end, Milo succeeds by dodging a lot and by being clever. I love this, because it breaks tradition and doesn't break character.
So there. Awesome writer, awesome setting and plot, geekness all over the place, and a hero that is impressive not for amazing skills but for an unyielding belief in doing the right thing. So go watch it. Atlantis is waiting.