I think "Emissary" was possibly the best Trek pilot. It made me curious to find out how this show was going to work with the non-starfleet characters playing prominent roles in the series. Also, I immediately sympathized with Sisko because of his ordeal losing his wife, and I understood the animosity towards Picard because as TNG fans, we found it very easy to just brush off the deaths that must have taken place because of Locutus. Picard wasn't in control, and that made it okay from the audience perspective, but what about characters who were personally affected by those turn of events. Do they have some right to despise Picard for what happened? Perhaps not so from the audience perspective, since we are conditioned to sympathize with Picard, but how would we feel if it was one of our own loved ones lost in such a way?
It also followed up on what's going on with Bajor, and introdruced the concept of religion in the trek universe without making it partronizing or holding it up as something that needed to be debunked. Plus, the whole premise that the station would become some sort of crossroads with the discovery of the wormhole made it seem like it was going to be an exciting show.
The plot of the episode itself was slow paced at times, but for the most part I was drawn in. The only things that made me wary was that I wasn't sure I liked seeing a Ferengi as a main cast member and I didn't quite like Dr. Bashir. It took a few episodes for me to like Quark. The Quark-Odo interactions were the best part of the deal.
As for Dr. Bashir, I actually don't think I liked him much until the friendship with O'Brien blossomed. He was just too smug and too green for me to like him as a character. The whole Garak relationship disappeared in the 1st season, so there wasn't much of that to look forward to early on. By the 2nd season, I started to like Dr. Bashir. I think "The Wire" went a long way for many fans in solidifying the fact that his character belonged there. As the show went on, I really, enjoyed and looked forward to shows where Bashir had the A-story.
Comparing "Emissary" to "The Man Trap" (1st episode of TOS to air) and "Encounter at Farpoint,""Emissary" does the best job of introducing the key characters and establishing the tone for the rest of the series. "The Man Trap" was a Dr. McCoy episode which was a great stand alone episode, but certainly not the best episode to have as a pilot of a new show before anyone heard of Star Trek. EaF was okay, but a little too drawn out, and not that much of a payoff at the end with the station being a lifeform and Counselor Troi all in tears at the end. The whole purpose of that episode was for Picard to prove that human beings were not savages by not firing at the lifeform and uncovering the truth.
"Emissary" had the best mix of high concept elements, action, and drama. It wasn't perfect, but I think it got the job done.