I'd say the end of this two-parter actually marks the moment when Dukat and Sisko definitively become enemies. Up until the end Dukat sees Sisko as a potential ally in the sense that he perceives him as someone he might be able to manipulate successfully. Sisko proves resistant, though, so the battlelines are basically drawn from that point forward.
Having just rewatched these, it's Dukat who really shines. He comes across simultaneously as extremely charismatic, yet quite intimidating. The scene were the Maquis are trying ineptly to interrogate him is a classic.
They're good episodes for Sisko too, though, in the sense that they show him walking that thin line between loyalty to a friend and loyalty to Starfleet. Nothing groundbreaking, but nonetheless dealing with this conflict and Dukat at the same time displays a strength of character on Sisko's part. He has to navigate the temptation to give into either his friend or Dukat. In the end he does neither.
Cal is basically just a mirror image of Sisko, so there's not much to say about him other than he serves his purpose.
The other scenes that stand out are the ones between Sisko and Kira, who empathizes with the Maquis. I'd forgotten about this aspect of these episodes, but it's a actually a pretty substantial development in their relationship as well, in the sense that Sisko's "it's easy to be a saint in paradise speech" brings him to a better understanding of how Kira sees the world, as well as the Maquis.
Overall, better than I remembered. The main weakness is a certain stale quality in the interaction between Sisko and Cal. Their relationship feels overly rehearsed and a tad lifeless.
Sisko hates Dukat's guts at the start of "The Maquis" (not surprising, since the last time Sisko saw Dukat, it was the episode "Cardassians" when he found out what Dukat did with Rugal just in order to hurt Kotan Pa'dar politically, and if Dukat ever seemed like an absolute bastard, it was in that episode). He shows his animosity towards Dukat very openly when Dukat first appears in his quarters (granted, the way he is just sitting there waiting for Sisko is pretty creepy), and even seems scared that Dukat might have kidnapped Jake! But throughout the two-parter, they develop a more complex relationship as unlikely allies - which continues in a similar way "Defiant", and will only finally come to an end in "By Inferno's Light". They even almost-friendly conversations about Dukat's children in both "The Maquis" and "Defiant", where Sisko seems to see Dukat in a little bit different light for the first time (it's funny that he is so surprised to learn that Dukat has children - why wouldn't he? - but I guess people can feel strange when they see someone they always thought of an enemy/bad guy is also a person with family, parent etc.). And there's that scene when Dukat bluffs the freighter captain into surrender through sheer attitude, and both Sisko and Kira look like they can't help being impressed (Kira was herself also great at getting people to back down through attitude - see "Emissary" - and Sisko will develop that kind of badassery later on 
).
