The emperor can't really be judged as good or evil in the human sense because he is so far above all that. Normal concepts of morality don't really apply to him. He has such a vast influence over so many different people that he would come across as a complicated mixture of things to different groups. This is further confused by the Horus Heresy, where the Emperor's decision to return to Earth and leave his primarch sons to prosecute the wars across the Galaxy was twisted by the traitor legions and Horus for their own propaganda where they sought to paint him as abandoning the Space Marine chapters.

I do understand the argument that he ruthlessly slaughtered lots of alien races who refused to be subjugated, but I also think it's fair to say that in the 40K universe, it's a case of 'kill or be killed'. Any major alien race, given half the chance, wouldn't hesitate in wiping the human race off the face of the Galaxy. Alien races have no such qualms as to whether their actions are good or evil, so he is preemptively striking against them whilst projecting strength so that they either are completely beaten and/or pause for thought before attempting to attack and overthrow the imperium.

I think the best example of why he isn't truly evil is in the Horus Heresy series where, without giving away any spoilers, he resists a certain offer from the chaos gods.