firstly, id like to add o to what COTE said, most primarchs with relatively few exceptions (Angron, ferrus,russ and mortarion) wouldnt mind/welcomed the idea of retirement for example Guilliman and corax. (Curze i dont think would really mind, i mean he would go insane and kill anyone who broke the rules, but he should on the whole be a benevolent leader of his sector/planets/empire, as he was on Nostramo before the Emperor came).
secondly, there is the webway it needs to be cleared out, the eldar killed and the other xenos species, such as the Necrons, the tyranids would also of course eventually become a threat.
furthermore, there are (Well were) entire sectors of space such as the eye of terror, the remotest reaches of the galaxy (that were previously inaccessible due to the fact the light of the Astronomican could not pierce those areas.), places with warp anomalies that would have to be cleared out.
the legionaries Astartes, would curb their conscription rates, simply maintaing their numbers with no wish to increase it.
Russ and Angron, would no doubt probably create their own wars, if i was the emperor i would simply create entire deathworlds, the type that could kill even the most battle hardened astartes and let the world eaters play there for a few millennia.
ferrus would most likely become an emissary for Mars delving into the farthest reaches of space/the webway for the martian tech priests and recovering various artifacts.
i also think, if conquering the galaxy went really well, the Emperor would set his sight on the universe.
Magnus would be content to be on the throne, he can guide humanity to its destiny, he would learn everything there is to learn.
i8 personally agree with Sigisimund, no matter there will always be war, the gods of chaos would still fight, tooth and nail, and they would see the imperium as a threat like none other, no doubt they would combine there powers and set aside their rivalries for an unprecedented amount of time, pooling their power, creating new species, new possibilities and chances for corruption.