@Vikram at the worst possible portrayal of skulldad, the whole 'organic machine' thing, he was apathetic to plight/suffering. To him, it was unimportant in the greater picture, which is the survival of humanity/defeat of chaos or whatever. After everything was done and over with he would slither into the shadows and let humanity rule itself.
In contrast:
I'm not calling the Emperor a good administrator -by any means- but he planned for the Imperium to exist without himself at its stead:
At the end of
Horus Rising, after Ullanor, there's already a civilian council set up, sending a delegation of administrators across the Imperium, insisting to Horus -who recently became Warmaster- that Terra has to begin collecting tithes from its worlds, to which Horus replies that most of the instated governors are on worlds still in compliance, still rebuilding. The head of the delegation, Aenid Rathbone, claims that it's the will of Malcador the Sigillite and the Emperor. After she leaves, Horus says that people like her will be the death of the Imperium, not its myriad of enemies. He says:
We can infer from the above that the Emperor has too much faith in the general populace. He's already ceded a degree of power/autonomy, Horus at this time is fairly trusting/loving of the Emperor, and spent most of his formative years under his tutelage, I would assume he knows the man well, personally.
Technically, one can argue that the Emperor didn't care about the Imperium personally, since it's just a means-to-an-end, but that's stretching it. When he was struck down and interred on the Throne, the Senatorum Imperialis took up governance of the Imperium, with the help of Guilliman's reforms. When Palpatine died, on the other hand:
In his 40k years of life, the Master of Mankind has never done anything
nearly as... sheerly, pettily evil as Operation Cinder. GEOM has done stuff such as slavery, anti-religious pogroms, state-enforced destruction of mixed human-alien civilizations. But Palps wanted to burn down
everything out of sheer spite.
To contrast, again:
The stance of both Empy and Palps on aliens is contradictory, so I'll ignore it.
Emps turned humanity from the certain prey of alien species like the Nephilim, or the chattel of Chaos, into the dominant force of the galaxy for 10k years, and is keeping the universe from falling into eternal damnation.
Contrast that with Palpatine, who basically wants to become a Chaos God and cover the universe in the darkness of his shitty rule.