You can't very well blame the story on Disney; it was a direct adaptation of Robert Louis Stevenson's novel, which was and remains a classic. If you don't like the animation, you're welcome to your opinion of course. For my part, I particularly enjoyed:
* The scenes in which the cyborg was using his mechanical appendages to help him cook.
* The opening sequence in which Jim Hawkins is riding his pseudo-windsurfing board.
* The scenes in which Captain Amelia jumps from spar to spar to personally inspect her ship's rigging (not to mention Emma Thompson's execution of the voice work).
* The entire premise of adapting the visuals of wind-powered vessels to a high-tech spacefaring universe.
Though I agree with you on the other films you list (at least, the few that I have seen), I persist in my opinion that Treasure Planet was good art.
There is a huge difference between visually stunning and a good movie.
Cars 2 was amazingly visually stunning, but a horribly average at best film overall.
I agree with you that Treasure Planet had some amazing visuals, but it wasn’t a great film, it was mostly forgettable, which is why you can find it in the discount rack and playing on disney jr for free 3 or 4 times a month.