He is to become a god once he ascends from the golden throne. A warp entity of terrible power. He will then be omnipresent throughout the Imperium and beyond, and none shall hide from His gaze. Traitors will suffer like Eldar did during the birth of Slaanesh. The occurence of "divine interventions" in moments of dire need will increase. He will be able to influence the Warp, to control Warp storms and other events. Gods of Chaos shall tremble.
Modern 40K fluff has completely killed any idea of the GEOM not being the GEOM and instead the EOM. Imperial Daemons are a thing, acts of faith cleric powers are a thing, miracles are a thing, personal visits from the Emperor are a thing, etc. He's flat out a gestating warp god.
It seems to me that the Sisters of Battle and all their surrounding miracles settle this issue. Sisters and other believers in the divinity of the Emperor can even "ascend" into Angelic-like beings - not unlike Daemon Princes. And then there are the mysteries of the ghostly Legion of the Damned and Sanguinor. I'm sure there are other examples that I'm missing. Oh, the Emperor's Tarot. That too.
The God Emperor of Mankind is actually a really cool guy. The 40k wiki has a great (if long) article on His origins and deeds.