I like to think the real reason has not been revealed yet. There are several "Psykers" of different species (namely the Eldar) that might have even posed a threat to the Emperor. For instance he was working very hard on developing parts of the Eldar webway for Humanity. (Presumably the Eldar figured that stuff out before the Emperor's balls dropped.) Also it is specifically stated that if Humanity had not expanded that the Earth would be prone to Xenos and/or Chaos influence.
I do not think the Emperor was the most powerful Psyker, he was certainly not as gifted in foresight as he thought he was. Blinded by love for a son...REALLY? Considering the way some of the Emperor's son's were treated it sounds like the Emperor just liked the first Primarch he found the best.