Wait a minute. Why couldn't Arceus have done anything himself about Cyrus?
1. He's an Eastern conception of the creator god, very powerful but not omnipotent like the modern Western conception, and 2. He works in mysterious, Ash-centric ways.
OBJECTION!!! If he can create the Poke-gods of space, time, and antimatter, then stopping ONE human from doing something stupid should be easy for him.
Author here. Basically, he didn't notice until time was already imploding, so was somewhat limited in his options. (Watsonian explanation). Or, for the Doylist explanation, it's the reason for the time travel to set the plot off...
Oh...Also, are you going to continue the fic past Black and White?
Oh boy. How's Saphroneth going to get around the introduction of the Fairy type?
He did recognize Genesect, so perhaps sometime past that movie is another possibility. During the film he had absolutely no idea what it was after all, yet he could tell what it was in Misty's battle in the center of the mind
Plus, he also knew about the 'other' Mewtwo which was involved in said film. So it would be after that, but before X/Y.