Waltz is an underappreciated gem, probably because the direction taken with Dukat's character from here on is unpopular. Brooks and Alaimo both give excellent performances, and Moore's script is the most probing examination of the psychology surrounding the Cardassian occupation of Bajor since Duet, to which Waltz is consciously a sort of sequel or follow-up. One can debate the merits of using Kira, Weyoun and Co. to express the various facets of Dukat's fragile psyche, but I think the device works to good dramatic effect. It especially helps to have Kira around mocking Dukat, which is his worst nightmare in a sense: he fears her contempt as much as he desires her approval, and that of all his victims.
Often in the later seasons of DS9, you can hear the writers talking and arguing with themselves. For whatever reason, probably a result of the creative struggles that DS9 faced in its quest to deconstruct and escape from a legacy of trek clichés, the scripts in the later seasons tend to break with suspension of disbelief and provide us with a window into the creative process. In Waltz, there's Sisko's line: "Do you really want to do this? Alright, let's do it!" (or words to that effect), which is like a fragment of the discussion/argument that produced this episode: do we really want to go there with Dukat and take a serious look at the psychology behind his patronizing attitude toward the Bajorans?
The answer is "yes, let's do it", and the results are pretty satisfying, especially the lines about the Bajorans wearing their pride like a badge of honor and Dukat hating them for it. The first half of that statement is a perfect description of Kira in particular, and explains Dukat's fascination with her, which is sinister and sincere at the same time. These parts of the script probe quite deeply into the latent racism and hatred that drive the colonialist mindset and that fuel Dukat's obsession with winning the Bajorans' approval and even worship. He needs them to "recognize his greatness," as he says in Sacrifice of Angels.
The overwrought ending and Sisko's final line, which feels like an unnecessary attempt to tell the viewer what to think, only slightly undermine a powerful episode.