One question : who is the new Emissary - Kira or Vaughan ?
Well, I'm kinda guessing that the whole point is that they don't need an Emissary anymore. From the Prophet's POV, Sisko was basically there to save Bajor from the Dominion, the pagh-Wraiths and the Ascendants. Once that was done, they didn't need him anymore. So I don't think Vaughn or Kira are "the new Emissary," because I don't think there is any Emissary at all now. Especially since Vaughn is now full-on flat-out dead.
I do, however, enjoy how Vaughn's storyline ended up tying in so beautifully to developments in my own fan-fiction that I wrote before ever reading these books...