I have to admit that had I not read these as an unofficial trilogy:
Rough Beasts of Empire / Plagues of Night / Raise The Dawn
I likely would have been far more irked with DRGIII. The problem isn't RBoE isn't good, it is and it conveys what's going on extremely well, but watching Sisko tear himself apart isn't at all pleasant. Knowing there's the next pair that continue the story, with RBoE as the descent part of the arc as it were, greatly defangs this problem. As take away those 2 books and the reader is uncertain as to what's next, which coupled with what seems to be pop culture's tendency towards darker and darker stories and I could see why people would be severely cheesed off.
But being able to go straight into the next duo sidesteps all of this as that duo deliver a great many surprises. While there is the destruction of the station - and those scenes are utterly excellent, where the duo shines is in the portrayal of recovery. The recovery of Sisko, but also of the Federation. They also bring a maturity to the Typhon Pact and the Romulans are especially well done, Kamenor being particularly good.
It would have been very easy for Pocket Books to opt for another big war, to have the Federation + allies versus the Typhon Pact, but in not doing that they actually make the books stand out far more and in a positive fashion to boot!