A common thread on here has been "why would God do X and not any other thing with the universe?"
The short answer is "we don't know".
The full answer is "we don't know and maybe we'll never know. Possibly we can't know."
To many a mind that looks like epistemological defeatism. Those trained in hard sciences may especially regard it so. Hard science rarely admits not to know something, and when it does, it proposes that we will know one day, usually sooner rather than later, and that surely we CAN know.
These are two very different, even contrary, approaches to knowledge within a field.
But the former is consistent with the field studied by theology. If we are studying something which is by definition immensely more intelligent than ourselves, it should be clear that we must expect not to grasp the reasoning behind some decision or another. The highly trained chess player takes decisions whose reasoning is entirely mysterious to the newbie or casual player -- even one who knows the game rules just as well. That the newbie cannot grasp why, or would make a different move, doesn't mean there is no why or that the move done by the master doesn't make sense.
And this is a difference in practice more than in intelligence: a just above average expert player is way more proficient in chess than a guy who is top 0.01% of all IQs but a newbie in the game. Now picture what happens when the difference in intelligence is much, much wider, and where the difference in practice also favors the smarter guy.
Why should minnow intelligences like us (because in that perspective, that's what we are) understand in any depth the acts and choices of an intelligence as high and comprehensive as to be capable of Creation as we define it?
Romans 11:33 [ISV] O how deep are God’s riches,
I don't ask for faith from whomever that faith doesn't come naturally to. But to present an argument of "I would do it differently" when precisely one of the reasons God is God and man is man is the difference in intelligence (call it wisdom, experience, practice...) is really the wrong way to do it.
The Black Plague lasted for longer and killed more people in Catholic Europe because its aetiology (Yersinia pestis) was unknown; its treatment and prevention was based on Humor Theory; rats were not recognized as vectors; corpse disposal was not just inadequate, but outright increased the danger. If we transplanted an European, even an educated one, to today, and told them that bleeding and avoiding baths make the disease more dangerous, that corpses and things in contact with the dying patients should be burned, that cats and snakes should be intently reproduced to hunt more rats... the reply would surely be that they would do it differently. And here we're just talking about the increase in knowledge from 700 years past; as the difference in intelligence isn't really proven (though the Flynn Effect hints there may be one).
To summarize: yes, some things may make no sense to us. But that doesn't mean that they make no sense to an agency with much higher intelligence and much longer experience than we (even collectively as 7bn hoomins) have.