You know, it baffles me, too. I'm going to be honest here - I don't think that I've ever read Treasure Island. If I did I was young enough to forget it. Having said that, I was really impressed with how the story of treasure planet stuck to the key plot elements of the story that I have seen in two live action versions of Treasure Island (the disney version and a more recent Australian version). In fact, I thought that they did an excellent job of tightening up the story and picking up the pace as compared to those live action versions. One of the things I enjoyed about it was mentally comparing it to the live action versions, and it came out ahead, to me.
I really liked the story. I tried watching the ice age movie twice, but I couldn't stay awake through it either time. I am not sure why anyone thinks it had a good story - it seemed to me to be a pretty basic traveling buddy thing, with a big guy and a little guy. I thought it was sufferingly lame. Let's see Emporer's New Groove was funny, Road to El Dorordo wasn't very good but the gay allusion stuff was funny, but this one didn't stand out to me. It was like Fox said "Dreamworks is doing a traveling buddy movie set in historical S. America, Disney is doing a traveling buddy movie set in historical S. America, and Disney is also doing a dinosaur movie...let's do a traveling buddy dinosaur movie, only not use dinosaurs..." I also thought that the animation wasn't that great. A lot of people must have liked the shorts with that squirrel thing trying to get the nuts because they kept making them, but they didn't seem that funny to me really.
I liked the story of Treasure Planet though - a young guy finds a father figure and then is betrayed by him, goes from being angry young guy to a hero. I thought it was good. I think some people were annoyed by the martin short robot, and so say the story was bad, but it didn't bother me. On the contrary, I thought it was an interesting way to match the marooned Ben character from the original story. I even sort of like the music they threw in to try to attract the tween girls.
I also thought it was visually striking. I have heard an argument that adventure is a format that doesn't transfer to animation, because you know it isn't real and so never really feel tension worrying about the characters (Princess Mananoke, Vampire Hunter D etc. besides, I guess). I don't buy that though. I sat through XXX on the flight over here and I never felt any tension for any of the characters in the adventure situations. It didn't feel any more "real" than any animated movie. I thought the action depicted in treasure planet was thrilling and exciting in its visual impact (e.g., the flying surf board thing). I thought that the animation was as striking as anything from Fantasia 2K really. And Princess Mananoke for that matter.
I also think that treasure planet was hard for a lot of people because they couldn't get over the idea of old looking ships in outer space; that never bothered me, it was obviously fantasy - I enjoyed it. But then I liked Atlantis OK too, I thought dinosaur was visually stunning, and I laughed out loud to Emporer's New Groove, so I'm probably just an idiot. I guess Disney should put more focus into girls 3-8 and boys 3-6 and have more jungle book 2s. I don't know.
In American culture currently, there is a point of view that animated movies, and disney movies, are for little kids. And so older kids want to break away from that. Over Christmas I was watching TV with a cousing who is a 13 year-old-girl. A commerical for the Beauty and Beast DVD came on and I asked her if she wanted it - of course not, she liked it when she was a little kids but was far too old for it now. Later a Monter's Inc dvd commercial came on, and she admitted that she really liked Monster's Inc. I think the computer animation / traditional animation is sort of covarying with it. Tweens see computer animation as cooler, and traditional animation as more suited for younger kids. A lot of adults are the same way. There are many who have a young kid they will take them to most any G rated animated movie because it is kid's stuff.