This is the commonly held mistake; based usually on a belief in Freewill that comes from nothing but subjective experience (ie: feeling that we have Freewill, assuming it exists, and then saying God also has it).
In truth though every being acts in accord with its nature; and that includes God as well.
God creates the universe that is real; the only one that could ever be real. The universe is this way because this is what a real universe means in practice (as opposed to numerous half-imagined fake ones that we can partially conjure in our minds).
So if something occurs in the universe it is here because it has to be and could be no other way. This is what a real and orderly universe means in practice. One which does not contradict itself and in which cause leads to effect. 1+1 cannot equal anything other than 2.
Is this a limit on God's power? No. It is no limit on God to say He can only do what is real and what is consistent with cause and effect.
So to answer the OP's question....God made the universe this way because "this way" is the only way it ever could have been, because "this way" is what real means in practice.
God did make the universe exactly the way He wanted it. The thing is, He didn't want a bunch of robots. Not even the angels were made without a choice.
Men can make machines that serve us. Hammer, saw, coffee maker, car, computer... but they all do exactly what they are meant to do or told to do.
Then men try to work fail safes into them so they cannot hurt us. Safety default switches, guarding, etc. Then we built in systems that stop other unwanted people from using them, key codes, passwords and other interlocks to protect form theft, sabotage, or disclose secrets.
We are a creation of God. He made us with our own ability to accept Him or reject Him. No safeguards, no pass codes, no key interlock, no mandatory procedure. He wanted us to want to serve Him out of our own free will and loving attitude.
Everything else in this world WAS perfect. Until Adam and Eve chose to use their free will and do something they were told not to do. They also knew what would happen if they did.
Now the universe is coming apart, greed, sloth, hate, selfishness.... It's all causing the dysfunction of this world. Each time, a civilization arose, came to power, achieved dominance, corrupted itself and fell. Each time the power was stronger, the reign was longer and the fall was greater.
Now we are at the last great civilization, the longest run, the greatest accomplishments, the strongest of might and power.... And, now comes the fall....It's all out there to read for yourself. It's inevitable. Only the ones that have humbled themself to Christ and accepted the gift of salvation and have the faith to believe, will survive this one.
If you cannot even accept the simple things of God's plan and change your attitude, how do you expect to see the big picture?
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