Again, you saying "most of the time he spent in Sol was doing wars and then he immediately did more wars instead of building solid institutions using his super-brain and magic powers" is you admitting he's a bad ruler. Sure, maybe doing the Crusades a bit slower would have meant a slightly smaller Imperium,
No, doing the crusades a bit slower would have had resulted into the Orks evolving back into the krork, producing war planetoid, and enslaving the galaxy(1). Or the Rangdan expanding and enslaving the galaxy(2), or any other expanding hostile xeno empire enslaving the galaxy.
(1)We have an example of an ork on the cusp of evolving into the Krork: The Warboss of Gorro which was strong enough to murk Custodes and was throttling the Emperor until Horus backstabbed him.
Another example of what happen if you leave orks to evolve is The Beast: aka Orks strong enough to throw down with primarchs with Attacks Moons and War Worlds with gravitic weapons powerful enough to destroy planets.
(2)The Rangdan were kicking the imperium ass hard enough that multiple legions of astartes were savaged(the dark angels lost their spot as the most numerous legion, and the death guard had to do emergency recruitment procedure).
To give examples of the emperor desperation:
a) The Emperor focused only on this front of the conquest for 60 years of the 200 years long Great Crusade.
b)He unleashed a shard of the void-dragon(a star eating vampire machine god) to fight them.
c) He blatantly broke the treaty of Mars by revealing he had Advanced warp-tech(and he had forbidden the mechanicum to study that field) on a Titan Legion that were under his direct order(All "God-Machines" were supposed to be under the order of the mechanicum). Call the Emperor a caveman fascist dictator all you want but he smart enough to not alienate an allied institution who supplied all his weaponry, supplies and ships.
d)The Rangdan needed three different campaign to no longer be a threat.
Tl;dr:The emperor simply didn't have the time to be a good ruler: The entire imperium in 30k is an emergency stopgap he would have purged at the end of the crusade. You simply don't treat the booboo on someone toe if he is currently dying from a massive gut wound.
In the Diasporex, a human-alien nomadic federation's own words: The final words of the alien captain were "We only wished to be left alone"."
That was the problem: they had fleets of ancient warships in an universe where ancient his better and refused diplomacy and lived as nomad. Letting them be would let a dagger be pointed in the back of the Segmentum.
Tl;dr: You don't let unidentified fleets that don't answer to your call in your territorial waters.
