Big E is the central figure of the 40k setting, which makes sense given the game's human-centric perspective. He founded the main human faction and led it to galactic hegemony. He also inadvertently played a part in making Chaos the threat it is today, by creating conditions that led to the Chaos gods gaining countless mortal followers. Not to mention his vast psychic power, next to which even Eldar farseers pale in comparison, and which allows him to keep the Chaos gods in check even while comatose.
Szarekh, though...
Szarekh does not just keep the gods in check.
Szarekh declared war on the gods... and won.
He shattered gods who were far older than the Chaos gods, older than any sentient races. Then he imprisoned and enslaved their remnants.
All without an iota of psychic power. Without any gift of precognition.
Granted, it was really the Necron race as a whole who accomplished this great deed, and they did so at the height of their power, which was millions of years ago. It's also been said (though it might be false) that the mysterious weapons they used to destroy the C'tan no longer exist. Even if those weapons could be recreated, they are not guaranteed to be of much use in this age of the universe—they were intended specifically to destroy the C'tan, whose nature is wholly different from that of the psychic gods who now steer the galaxy's destiny.
Still... I think that in terms of accomplishments, Szarekh dwarfs the Emperor. It is him that Abaddon and the Traitor Primarchs should worry about, not the corpse on Terra, and they'd realize that if they got over their daddy issues. The Silent King is the true ruler of the Materium, and perhaps the galaxy's best hope against outside threats such as Chaos and the Great Devourer.
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