I read the 25th anniversary edition of ACO, which Burgess wrote a new intro to. He actually is proud of his story. What he hates is the version that was originally released in the US, and which was adapted into the Kubrick. Apparently, the editor (according to Burgess, the editor strongly disputes this) cut the final chapter in the US version, so instead of a book in 3 parts, each part with 7 chapters, there were 2 7's and a 6, both breaking the symmetry and killing the redemptive part of the story. Burgess' problem with that version is that nothing changes, no one learns anything, and the world is all the worse for it. In the original 21 chapter version, the final chapter sees Alex grow up.
Personally, although I see Burgess' point, I think Kubrick's movie is a goddam masterpiece, and I'm glad it is what it is. It's not Burgess' story, but it's a good story nonetheless. Still, I can't imagine how painful it would be to create what you consider a great piece of art only to have it ripped to pieces by others. I guess any author who options a movie might suffer the same fate.