he knows which designs are good and which are not.
Yes, but it's not as easy as that.The flaws of mortality are because of mortality, a process we must go through in order to become perfect. perfection is not an immediate, nor even an interim goal. Reaching perfection is the whole design conclusion of mortality, not its initiation. And, it is a mater of personal choice, not divine compulsion. If we are designed with perfection already intact, what is the purpose of mortality? If perfection is our state from the beginning of mortality, what purpose is there in having free agency; the God-given right to choose? After Adam is created at the conclusion of Genesis 1, and before he creates Eve, Adam is given charge to tend the Garden, and he is told by God that he may eat of every tree in Eden [Genesis 2: 16]. However, of one tree, that of the Tree of Knowledge, he may not freely eat; he is given the choice to do so, or not. It is the only tree in the garden that carries a condition on eating from it: "...for in the day that thou eatest thereof thou shalt surely die." Adam is given a choice. There will be a dire consequence to eat of that tree before he has experienced mortality. Experience first, mortality. Experience first, dominion over the earth [Gen. 1: 26]. Then, only then, in that proper order, comes perfection. It is a goal to be accomplished, not a skill to be had immediately. IOt is accomplished by making correct choices. It is hindered by making poor choices. The Tree of Knowledge is the figurative representation of the proper order of mortal tasks toward perfection, not to be had all at once and from the beginning.
That's... "Why would God create flawed beings and then a subsequent process that goes through many iterations (some of which were defective) when he already knows what the end state — "perfection" as you put it — looks like?" Because God knows what that end state looks like and is, but man does not yet know. He must learn it, step by step, having both success and failure along the way. Hopefully, more and more success rather than more and more failure as we progress. It is a matter of our choice by free agency.
We complain that because God gave us free agency, there is misery in the world. But what misery is there that we, collectively, do not cause ourselves? War is our doing. God commanded us to love. Pestilence is our doing, God commanded us to be clean. Disease is our doing, by introducing things to our bodies we should not when God commanded a proper diet, such as avoiding the fruit of the tree of knowledge until we are ready and prepared to eat of it properly. Drinking, smoking, drugs, even fast food and all the rest. Does anyone force us to consume these things? Nope. Our choice. And such things introduce foreign matter into our bodies that do the body no good whatsoever. The CDC says that 60% of cancer and diabetes would be prevented just by our making better consuming choices. 80% of heart disease obliterated, just by making better choices. So, why do we blame God for our choices? Why do we blame God for these miseries and others? He is not the cause. We are by our own poor choices. Who knows by what miracles great storms would cease if we were more obedient to God's laws than slaves to our own petty choices? Want to be perfect? Then be perfect by making proper choices. Yes, it;'s hard. It was meant to be. Satan's path is the easy path, and the reward is like unto it. He is the counterfeit, not God.