Some would ask, how could a perfect God create a universe filled with so much that is evil. They have missed a greater conundrum: why would a perfect God create a universe at all?
Ah, there it is, and that actually helps to answer the question. Assuming the Biblical God, canon states that God is love. So why would a perfect God, who is love, create a universe? It seems most likely to me that it would be so He can have an object of His love.
But what is love directed to something perfect and easy to love? That's hardly a worthy effort. Might as well make something authentic. And since He isn't just loving, but love itself, He might as well make it in such a way that He can carry out every aspect of love - love when they love you back, love when they turn away, love when they hate you, love when they don't even think you exist, and so much more.
The universe must be filled with evil for half these situations to appear, but it's not love to make someone evil. The solution? Free will. God made it so His creations were free to turn their backs on Him, but still, in love, He gave every warning against it, because separation from God is not only evil but death.
I never thought Alpha Centauri would be an answer to a philosophical thought experiment but the writing was brilliant enough to have already looked at this question 20 years ago. Good find.
We haven't, but there's this thing called "hierarchy". There is God, and its subordinates (angels, archangels, etc), and all the way under theres us -- humans. And below humans, the rest of the Gods creations -- dogs, cats, etc. And the logic behind this is diversity and beauty. And yes, even on a flaw (suffering, as mentioned here like a some sort of Gods curse rather than our "natural flaw" "why we suffer?", etc) can bestow beauty on its own. Why? Because everything have sense when we acknowledge that God is behind all suffering -- no matter how critical it is.Because He is Our Father, and The One and Only. We are His Children, and in suffering is how we learn that we are flawed and we need His Guidance.
I kinda tried to avoid being "biblical", but I had to in the end, heh.