Davem, I bring you back to what I said earlier.
In my opinion, Tolkien is trying to make the point that for us to have free will, there must be flaws in the world. Whether they come through Men's fall or through deliberate Creation of Flaws. Without Evil, we cannot make the choice to do what we will.
But still, ultimately the flaws are made up for and all get what they deserve, whether that be to live in bliss with God / Eru, or to suffer eternally. The choice is left to the peoples of M-E, that is why Eru created the flaws, but yet still makes up for them in the end.
That, I think, is the essence of Christianity, if the world was without flaw, we would all Love God from the moment we were born and it would not be anything special. God Loves us from before we were born, that is something special. But if we are given the choice to Love God or not to, then if ones choose to Love God then that connection becomes more intimate and special to the person.
So, I believe that Eru was making the flaws to give the people a choice, To have a special relationship with him, or not to, thus they were the most free of all races on M-E.
It is for that reason that I do not consider Christianity to be a religion, because the word religion suggests simply following a set of rules for life, where as in Christianity it is more based on having a loving and personal relationship with God. So we can guess that as Tolkien was a Christian, he will have wanted to get this message across to people.