Been reading "The Master of Mankind: War in the webway" by Aaron Dembski-Bowden. This is probably our clearest look at the Emperor yet.
Spoilers ahead.
Here we learn that the Emperor does not consider the Primarchs his sons, they are tools to him. In fact when speaking about them to his Custodians or other Martian Scientist...he refers to the Primarchs by their Number not their name. At one point there's a flashback to the Emperor examining Angron, and with the help of that Martian Scientist he confirms that the Butcher's nails have not only impaired his Primarchs higher brain functions, but cause Angron constant agony that can only be alleviated by aggression and violence. To remove them would kill Angron so the Emperor leaves them in, deciding that he's still a useful tool as is, and making no effort to alleviate Angrons constant suffering.
In fact he only allows them to call him 'Father' because he knows they wish to see themselves as more than the constructed warlords they are.
Then we learn the reason for the Primarchs, the legion, the Imperial Truth, the great crusade, really everything he has done going back to the conquest of Terra. The Emperor sees mankind is becoming a Psychic race, one with more potential than the elder at their height. So the only way to prevent mankind from having an even greater fall, is to rule it all and guide it. There can be NO enclave of hidden humans, that follow a path other than that of the Emperors because they would be a threat to the safety of all humanity. The Webway was meant to end mankinds need for Navigators and Astro paths and once that was done, the Emperor planned to sever humanities connection to the warp.
Some quotes the help you understand the Emperor:
"When the Imperium shields the entire species withing the laws of my Pax Imperialis, when humanit is freed from the warp and united beneath my vision, I can at last Shepard mankind's growth into a psychi race."
"Control, Tyranny is not the end, [Custodian]. Absolute control is but the means to an end."
"Humans need rulers."
-In response to why he held a celebrations at Ullanor-
"To honor the creatures that call themselves my sons. My necessary tools."
So...make of this what you will...but as far as I'm concerned "The Emperor is a Bastard"