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POSSIBLE SPOILER WARNING
You guys need to read "Mechanicus," then "First Heretic" and then "The Outcast Dead." Now time for wall-of-text and my chance to give you my full theory considering what facts we know.
The Emperor is - we can all agree - a singular being. There has never been a more powerful individual in entire universe (I don't consider the Tyranid Hive Mind to be an individual, but a gestalt consciousness and therefore on the same level as the Chaos Gods) and can be imagined as a man standing with a foot in both the material world and the immaterium. Due to his vast power and foresight, the Emperor traveled the length and breadth of time, seeing innumerable outcomes for Humanity (the last chapter of "Fear To Tread" is a perfect example of where a psykic with foresight sees varied outcomes of the future, also see the Eldar books). It was in the course of these ethereal travels that the Emperor saw that there was a slim path by which Humanity might be able to reach a point of apotheosis; to harness the powers of the Empyrean without fear of corruption from the Chaos Gods -- or at least at greatly reduced risk from them. Once he had determined this path he then set about making it a reality.
As it says throughout different points of the HH series, hints here and there, the Emperor created seeds within the socio-psychology of the human race. He created thousands upon thousands of myths and religious whispers that would one-day bear fruit and allow Him to step into the picture and claim suzerainty over all Mankind by self-fulfilling prophecy (pretty damned clever imho).
Once the Emperor took power over all of Terra (finally) and began the Great Crusade, he was prepared for the next step of his plan: galactic domination and the first step in eradicating Chaos.
Because the Emperor knew that Chaos was the primary foe against which Humanity must win, he set about cutting the Chaos Gods off from their main source of power: faith. The Warp is a reflection of reality and is fueled by the emotions of living beings in reality -- and the Chaos Gods feed upon those emotions, but even more so they feed upon the praise and worship that is offered them. By creating a galactic-wide Human empire that is ruled by secular thought and non-spiritual belief (with a strong undercurrent of faith changing to being put into the Emperor), the Emperor was -- in essence -- turning off a spout of water that the Chaos Gods required for sustenance. If he could manage to destroy the last vestiges of religion (many of which were twisted to worshiping Chaos in its varied forms) then that would be the great first step to fully defeating Chaos.
But the Emperor, beloved by all, failed in one thing: he underestimated the frailty of his greatest creations - the primarchs.
As I said before, the Emperor is a singular being -- none are as He is. In His mastery the Emperor forged 20 sons, beings unlike any other, but as close to the power of the Emperor as any other living being could become. They were to be his generals and crusade leaders, the exemplar of all the power and virtues of the Adeptus Astartes that were the gene-sons of their primarchs. It was his greatest and proudest moment of creation, when he bore the primarchs into existence. It was that -- pride and a mix of faith in his sons -- that was His downfall. Because the Emperor believed in his sons and thought them so far removed from the petty emotions that undermine the Human soul, he underestimated their fragility. Horus was not brought low by a promise of power or majesty; he was brought low by envy and a sense of abandonment.
In His effort to bring about an ascended Humanity, the Emperor put upon himself the burden of sole guardianship of that task -- only ever giving responsibility for lesser tasks to others when he felt it was necessary to concentrate on other, more important things (such as when he created the Order of the Dragon to keep the Void Dragon locked up on Mars; or made Horus the Warmaster to continue the Great Crusade). He was not able to relinquish the sense of responsibility that he felt in regard to guiding Humanity upon His chosen path.
This focus the Emperor had upon the chosen path for Humanity meant that he would miss various things and that Chaos would do everything in its power to oppose this plan. It is only with daemonic intervention and twisting of truth and lies that the primarchs are scattered in the first place (Ingethel manipulates the Word Bearers and preys upon their loss of faith in the Emperor -- and is capable of placing Argel Tal in a position where he can physically affect what was one of the most well protected locations in the galaxy, the gene-vault where the primarchs were forged and watched over by the Emperor himself).
And so the Emperor failed to fully understand his greatest creations (his sons), failed to fully educate them in the true threat of Chaos, and failed to share the burden of Humanity's path with any other. These combined to change the course of history and led to his placement upon the Golden Throne -- forcing Him to skip step two of his plan and onto step three: the creation of a religion based solely upon the God-Emperor that would find no opposition in a galaxy that had been cleansed of other religions. By being placed upon the Golden Throne, the Emperor ascended his mind and stepped fully into the Empyrean (no longer a man with two feet in two different places), taking on the responsibility of being a god-head figure and gaining the power from faith in the same manner that the Chaos Gods do.
Where it will lead from there? That's anyone's guess...
Considering all this, it's only natural that the Emperor would have a blind-spot in regards to his warriors. He expected so much of them and knew -- genetically -- that they were capable. The problem is that a living being is more than the sum parts of his genetic makeup.
