Maybe I'm just easy to please, but I had no problem at all with Dukat and the Pah-Wraith storyline.
If the storyline involving the Bajorian prophets and Sisko as the emissary had not been part of DS9 from the start, and then they introduced the Pah-Wraith/Bajorian prophets towards the end, as an afterthought, that would have been lame, but that's not what happened. From the beginning of the show, Sisko, in addition to being a Starfleet officer, was also a Messianic, Christ-like figure, serving the Bajorian Prophets. It made sense then, to have an anti-emissary/anti-Christ, working against Sisko and the prophets, and the obvious choice for the role was Dukat. If one watches DS9 from beginning to end, and looks at the Dukat/Pah-Wraith storyline in this context, one can see that it works. I thought that the last chapter of DS9 with Dukat playing the role as the anti-Christ to Sisko's Christ, was brilliantly executed.
Pairing Dukat up with Winn worked very well. Given that these two great characters never shared any scenes together before, it was exciting and an interesting twist to see their fates intertwined in the end.
The writers took ageless themes of good vs. evil, Zoroastrianism, Judeo-Christian beliefs and symbolism and created epic television that truly took Star Trek to a whole new level. I thought that it was brilliantly done and not at all comic-book-esque. And it wasn't pseudo-religious or pretentious, i.e., Star Wars.