The genius of Kishi
I think the absolutely best part of the manga is that no one in the manga is just evil.
So far every major* villain become one because of the flaws of the world they live in. Orochimaru became evil because after seeing the horrors of a world war he came to despise the frailty of human life and fear of death made him strive to become perfect. Nagato was also the product of war which killed both his parents and his best friend which made him believe that the pain of loss was the only way to make people believe in the value of peace. Obito lost half of his own body and watched his best friend kill the girl he loved which made him realize that the way the world works is flawed (this is one of the more important ones and I'll talk more about it later). Even Madara was the product of a world which warps people's reality. Madara had fought his rival Senju clan for so long and sacrificed so much (Izuna's eyes that he took) that he could not go back to peace with the people who the circumstances of the world had made him hate for so long. Zabuza, Gaara, Sasori, etc... all of these villains had traumatic events in their lives which had distorted the way which the viewed the world. These are all broken men which are products of the world they lived in.
Personally I think up to this point Obito's "warped" view of seeing the world (which is how old Madara viewed the world too) is actually the most important, because it is sort of all encompassing. The fact is that the world is fatally flawed. I think the fact that Obito does not blame Kakashi for Rin's death is very telling of this point. To Obito, Kakashi is not to blame for Rin's death, because he is just another victim of the circumstances of our flawed world. This fits into the general trend of all the major villains of shippuden.
Therefore the moon's eye plan is a rejection of the flaws of the world in which we live. However, I believe that by having Naruto and the whole world fight against this plan Kishi is actually saying that completely rejecting the flaws of the world in which we live is not the best option either. I think that was Kishi is trying to say is that the tragedy in our lives and flaws of the world in which we live actually add something to them which is more important than having a perfect life. Think about it, what really is so bad about the moon's eye plan if it could create a perfect world? I think the answer to this question is that such a world would lack the kind of moment's which make our lives meaningful. I think that Kishi is trying to say that the flawed world we live in provide us with moments for the human spirit to overcome adversity which would be lacking in the moon's eye world.
That is to say that the genius of Kishi is that no one is just evil but rather they are just a product of the flawed world in which they are influenced by, but that living in this flawed world is also important because it allows the human spirit to overcome adversity which adds meaning to their lives which they wouldn't have in a perfect world.