I admit to enjoying both Treasure Planet and Atlantis. I rewatched them recently and think they’re both much better than their reputation suggests.
Treasure Planet, yes I agree. Atlantis, not so much. The world-building was too rushed, and I don't know about you, but I found Atlantis itself and the people who lived there completely uninteresting. And it doesn't help in retrospect that Avatar later did essentially the same plot, but with much more impressive visuals.
I've been pondering about this, and I think the problems with audience reception to animated science fiction comes down to what the average theater goer wants from the genre: lasers and things blowing up. High tech but somewhat antiseptic violence. No, I'm not saying that this is what all science fiction fans probably want, its just part of the expectations for general audiences, who just want good entertainment for an hour or two.
For animated films that mostly need to succeed with families, you can't feature the same level of violence that would be seen in a live action film (although The Incredibles came kind of close). You'd think it would be the opposite, but for some reason, watching the violent death of an animated character just seems so much more disturbing than the often sanitized deaths in live action movies (all those stormtroopers...). So, the easiest go-to tropes in science fiction for marketing to audiences needs to be toned down or eliminated when the film is animated.
Or maybe not at all. I'm just speculating here.
I don't think the problem is that Disney doesn't have the ability to make a good animated science fiction film, I just think it's an uphill battle to sell it to general audiences.