Next to the Enterprise series, Voyager was one of the worst endings I have ever seen in the Trek runs. The whole series was just mildly better than Enterprise. Hell, they had to shove Jerry Ryan into a skin tight suit to bump up ratings cause their writing was so bad.
As for DS9, I can't see how the ending spat in the face of Rodenberry. The whole series played on the fact of how fallible man can be. However "good intentioned" they were (i.e. Section 31) they were human. Alien's weren't all on the same page (Damar's rebellion against the Dominion and the Klingon's internal strife). The enemy was clever and ultimately not evil, just misguided in their beliefs on what "solids" were about. Both sides commited pretty dispicable atrocities in the war. Even the concept of the prophets was fallible. They believed in preserving their way at the cost of all others, and Sisko did not. Maybe his choice to become one of them was so that he could change that perception by becoming one of their equals? They weren't apparently all omniscient (as Nightfall pointed out).