I don't think they are necessarily flaws, God just doesn't always deal with things the way we would expect. I think atheists have this idea that God is like math, and I don't see it like that. God just judges different situations. I believe it is fair in the end, but God isn't just like math. Why should God have to be like a math equation and make all justice equally?
One further thing to consider, God judges people, the entirety of their lives, God does not judge actions. When God judges people in the Bible, God is judging everything that they do, the perfections and imperfections. God cannot possibly list everything that everyone does.
So, I think in the end, when people see all of the ways in which God interacts with the sinful people, people will see that God uses a fair standard and shows no partiality, like it says that God does. But if God revealed all the information that God uses to make this distinction, the Bible would be 10000 pages long, containing the biographies and all related information of every situation that God judged.
One further thing to consider, God judges people, the entirety of their lives, God does not judge actions. When God judges people in the Bible, God is judging everything that they do, the perfections and imperfections. God cannot possibly list everything that everyone does.
So, I think in the end, when people see all of the ways in which God interacts with the sinful people, people will see that God uses a fair standard and shows no partiality, like it says that God does. But if God revealed all the information that God uses to make this distinction, the Bible would be 10000 pages long, containing the biographies and all related information of every situation that God judged.