The Emissary
The Compass of Terrestrial Dirctions, Volume 1: The Scavenger Lands presents multiple ideas as options for what the Emissary might really be. Although none of them seem quite perfect for my personal, home campaigns of Exalted, they did inspire me with their suggestions of variety.
I decided to keep a running list of alternate ideas for the Emissary, as they occur to me, although obviously only one of these is likely to ever be used in my multi-game's continuity:
Shalrina's Mask
The mask of the Emissary was constructed by the spirit Shalrina, Daimyo of Faces. She inhabits Nexus, currently, and perhaps she made the mask for the Emissary as a bribe for being allowed to stay in the city undisturbed. This can be combined with other ideas.
A Deathlord
The Emissary is one of the unnamed Deathlords. This idea came to me when reading the Resurrected Man option, and considering the idea of an Emissary with Void Circle Necromancy. Then it occurred to me that one of the listed powers for Deathlords is the ability to kill a mortal for a single point of Essence, which fits the descriptions of the Emissary killing people with a gesture. The Last Solar idea could be rolled into this, to a certain degree, if you assumed that the Last Solar was the personality who became the ghost which became the Deathlord.
Left Behind
The Emissary is the Ninth Minister of Autochthon. Autochthon left it behind in Creation when he took himself Elsewhere and made himself a workshop. As the ninth component soul of Autochthon, it would explain the being's great power. It would also explain his negative interactions with the Third Circle demon in A Day Dark as Night. It would also be a natural explanation for the entity's attachment to the idea of "the greatest city" as its domain.
The New Sixth Element
Alternately, the Emissary could be a sixth component soul for Gaia. This would retain the negative interactions with the minions of the Yozis. It would require that Gaia be experimenting with a "sixth element" though. If the element of "city" were a new project of hers, this might indicate that she knows Autochthon is dying and is preparing to take over that aspect of his being. This could be one of the explanations for the appearance of the sixth color of jade (yellow), although we already have the hints of one elsewhere.
Demon Summoned
The exacting by-the-letter behavior of the Emissary is suspiciously similar to what one might expect of a powerful demon summoned and bound to enforce the laws of Nexus. Imagine if some Celestial Exalt was responsible for the initial summoning, using the Emerald Thurible. This would allow the deed to be done by a Lunar or Sidereal, or a Solar with Celestial sorcery. Now, imagine that the Wyld Hunt kills this individual, and the Emerald Thurible enters the arsenal of the Scarlet Empress, and thus eventually goes to Mnemon.