pilot episodes are rarely the best in a series, because they have to to a ton of legwork to get you the viewer up to speed on all the characters, and setting etc
Agreed.
DS9's pilot did what it needed to do in introducing the major characters as well as Dukat. It got us familiar with the idea of having non-Starfleet characters as main characters for the first time on a Trek show. It got us introduced to the idea of a show taking place on a Cardassian-built space station as opposed to a Federation-built starship named "Enterprise". It got us used to the idea of the primary character (Sisko) as a single parent, and gave us some backstory about him....plus introduced the concept of the Emissary. Plus introduced Dukat as his chief nemesis.
It introduced the Prophets, the Wormhole, and gave us the basic concepts behind the religion and the religious hierarchy on Bajor as well as the basics of the Bajoran/Cardassian conflict and ongoing issues. Because never before had we had a Trek show which was tied so closely to a single planet and culture. And in DS9's case, we almost had two such planets: Bajor, and secondarily, Cardassia.
Finally, we had some action - through the Wolf 359 sequences, the wormhole sequences, and the sequences related to when they were moving the station.
Emissary had a tremendous amount of work to do as, at the time it aired, there had never EVER been seen a Star Trek show of this type. The TNG pilot didn't have nearly as much work to do - a Federation ship called Enterprise, a single captain married to his job, no non-Starfleet main characters, no Nemesis to set up...no particular planet to tie in, no religion to tie in. Nothing like that. It was TOS, only modernized a bit, was all. Not so with DS9.
Me? I'm thinkin' they didn't do so bad for 90 minutes worth of episode.
Certainly beats TNG's craptacular and extremely dated pilot.

And sets up the story just as well as VOY's pilot and ENT's pilot. Since TOS didn't really have an official pilot...well, I'm just not seeing what the beef is.