I fully agree that "Emissary" is probably the best of all the Trek pilots. I thought Sisko's interaction with the Prophets was brilliant, and as a baseball fan I enjoyed the way he used that game to explain the concept of linear time to the Prophets. There were definitely a lot of promising seeds planted in this episode, but like you I was a little annoyed that Season One kind of ignored a lot of them and went on a "TNG in a space station" track instead.
As for counters, what about some sort of "O'Brien Abuse" counter? I'm going through the show right now and I've noticed the writers seemed to love making O'Brien's life suck at every possible opportunity.