Thanx for watchin' =D
I have this W40k fantheory in which the God-Emperor of Mankind became a genocidal xenophobe due to manipulation by the Pre-Fall Aeldari and the Ruinous Powers. For most of his life, genocidal ideologies similar to his own Great Crusade- era murderous xenophobia would go completely against all the tenets of th religions and philosophies he founded while undercover. However, during the latter stages of the Dark Age of Technology, the decadent and sadistic Pre-Fall Aeldari realized that if nothing is done, then the God-Emperor will end up becoming like Myric or Nuke and while the uncorrupted Aeldari, Mankind, and friendly xenos will enjoy untold prosperity, any pleasure cults which survives the coming Group Ascension/Fall would be exterminated. Therefore, the Aeldari probably acted like late Age of Giants Nakai by manipulating the various other races (including Mankind) into fighting genocidal wars with one another replete with the sort of horrific atrocities which would astound the worst real-life war criminals both to prevent the rise of an imperium resembling the Union of WOrlds or Nuclean Ecumene and to entertain themselves. After the Aeldari fell, the Chaos Gods themselves found ways to subtly amplify the God-Emperor's feelings of despair, anger, and human supremacy sentiment so after a period of five millenia or more, Space Jesus slowly became Space Hitler (and Commorragh still stands despite all its internal strife).
By the way, the Union of Worlds and Nuclean Ecumene are two of my favorite fictional galactic empires and both may offer a glimpse as to what the 40K Imperium may resemble if the God-Emperor managed against all odds to avoid being manipulated into becoming a hardcore xenophobe.