The second half of "Emissary" relies a lot on lengthy scenes of Sisko's interrogation by the Prophets of Bajor - an idea that runs way too long. Michael Piller's insistence on using baseball as a metaphor for humanity is too heavy-handed. (Though I enjoyed the baseball references throughout the series.)
The other plot - Kira and O'Brien holding off a far superior Cardassian force - is kind of fun, with some fireworks. There are several jokes at Bashir's naivete, which was pretty egregious at this point in the series. That said, the on-station sequences feel like the setup they're intended to be rather than being great in its own right. Better stuff lay ahead.