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.
Animation Age Ghetto: A major contributor to the commercial failure of the movie. Some of the commercials try to avoid showing any traditional animation at all.
They themselves were seemingly unsure of who their target age group was. They have cutesy cartoony characters like Gune that are clearly aimed for kids, but they also have visible bloodshed and rather graphic onscreen deaths.
Awesome Music: Thewhole soundtrack. Even kind of counts in the ice field scene (where there is no music at all), as the absence of music makes the scene far more tense and effective than anything that could have been put in.
Crazy Awesome: Gune is undeniably loopy, but that apparently helps him a lot in his scientist/navigator duties.
Cale: I'll tell you a secret: This guy's nuts!
Korso: And I'll tell you another: He's never wrong.
Darker and Edgier: For all it's flaws, many fans were big on this movie solely because it was Don Bluth's first in years to be unapologetically intense and scary.
Ensemble Darkhorse: Gune, for all the reasons mentioned above, and because he is the only really Bluthy character in the whole show. Stith is a fan favorite, and oddly, Korso and Preed have gained a following, sometimes bordering on the Leather Pants.
Fan-Preferred Couple: Many people who watch the movie, nevermind if they enjoyed it or not, seem to ship Korso and Preed together. For others it becomes Squick because of Preed's appearance as an alien.
Ho Yay: Some scenes between Cale and Korso have this vibe.
Moral Event Horizon: Preed graduates from Plucky Comic Relief to all out evil when he shoots Akima through the shoulder as she and Cale are fleeing the ship. As if that wasn't enough, he leaves Stith and Gune with an explosive communicator which nearly kills Gune. It's ultimately satisfying to see the treacherous creep get his in the end.
Visual Effects of Awesome: Sure there is plenty of Conspicuous CG. But there's no denying the overflow of pure epic that is the Titan destroying the Drej and forming a new planet. Or the destruction of Earth in the beginning.
Woobie Species: Humans could be seen as this, as Earth was destroyed by the Drej, making humans galactic drifters.