After reading this thread I went back to watching it yesterday and have to say, YES, it is definitely the best pilot of any series. In fact, after watching all the pilots out of sheer interest recently, I find this, then VOY then ENT, strangely with TOS and TNG lagging in last as it just wasn't all that great.
Having finished watching the whole of DS9 about a year ago it was great to go back to the start and see where they all started from. When I finished the series, I wasn't really keen on the whole Sisko-Jesus-esque thing, but looking back on it now, it's clear that was being put in place even from the very start.
All of the characters start off leaving the viewer itching to find out their stories and intrigued as to where the series might go, Opaka started out strange but you warm to her, and Kira certainly set her stall out early.
Gul Dukat makes a great entrance and makes himself out to be shifty yet in a strange way likeable at the start.
scene with Picard and Sisko is really something after not having seen it in a few years. Sisko feels he is to blame yet Picard is still haunted by what the Borg did to him. Two great actors coming head to head, both on the same team yet one almost wanting to lunge at the other.
So much of Emissary seemed to make sense now having seen the whole seven seasons, in fact, I actually wish I went back to watch the pilot when I finished DS9 because a few things make that little bit more sense the second time.
Great intro to a fantastic series.