I gotta say, I think this movie deserves to be in the top 100. It's not a pleasant film, and it's not easy to watch, but I think it's subject and it's message are so relevant to today's society, maybe even more so than when the film was first released (though I wasn't alive then so I can't say for sure).
The first time I saw this film I had to stop watching during the attack on the writer and his wife. It's funny that I don't at all see this scene as more palatable by the inclusion of the song and dance. I found it then, and still find it now, to be extremely disturbing in it's execution. But I tried the film again years later and being prepared for it helped. I watched it to the end and for the next few days I couldn't stop thinking about it. I love when a film lodges itself so thoroughly in my mind.
And ultimately what I think the film is communicating is this idea of the way today's society plays on our psyches. Yes, the film is set in "the future" but it's very much about today. Alex doesn't care that he's doing anything wrong, and in fact he's just a symptom of a sick society. But by the end of the film he's gotten so much positive reinforcement from the scientists and the politicians (the last shot is extremely telling) that the most chilling thing about the ending is that I think he doesn't believe he's done anything wrong at all! He's been rewarded for his behavior. In a time where fame and talent don't necessarily go hand-in-hand, and when so many in society crave a spotlight for a substance-less existence, this film goes right at the heart of what creates these social paradigms.
As for Alex being the most sympathetic character... while I can't defend Kubrick's treatment of actors or his own mindset in this regard, I do believe that this has more to do with the simple fact that the film takes a subjective viewpoint rather than an objective one. Alex is "cool" and the most sympathetic character simply because we're in his head and he is the star of his own story. I think this approach is much more successful at telling this story than a more cinema verité sort of objectivity would've captured. In this light, it's easy to see that the other characters in the story are unsympathetic simply because that's how Alex views them. We're seeing the world through his eyes and it adds to the sense of distress we feel while watching the film.
So while I don't think this film is an easy or entertaining watch, I think it's an extremely important film that deserves to be seen and studied through the prism of our media-centric digital age.