Perfection of the universe includes us! Our bodies, our minds represent a being on the path to perfection. Indeed we are the mirrors of the perfection around us that is God (for lack of a better term).
When we can truly see the perfection that surrounds us is when we realize our own perfection.
To me perfection is a realization of the higher order that exists beyond Maya or illusion. It is this illusion that keeps us thinking that everything is imperfect. Our conception of God as perfect coincides perfectly with the idea that behind the illusion lies the true nature of reality and it is perfect.
There is the "cosmic dance" where everything is perfectly balanced. The only thing keeping us from seeing and realizing the perfection of the cosmic dance is our acceptance of the world of illusion as being real. So we are fooled by accepting the face of things as the true reality.
In this cosmic dance, even Nazism was part of the perfect order. Hinduism sees us reincarnating to learn lessons about morality. The Nazis created the perfect moral dilemma for everyone. Countless millions of decisions were made by millions of people. Eichmann made his, and people like Schindler made theirs. These circumstances always exist on this planet. This planet is like a classroom where we must learn our lessons or get left back. The goal is to graduate and thus free ourselves from this moral prison.
To free ourselves we must learn not to judge others based on appearances. If we witness a murder being committed and we judge just based on our observations, we really don't know what the motivation was, whether it was self-defense, etc. We just see a murder and want to condemn the person who did it. Likewise when we see any "crime", we are not in a position to know all the facts. This could include Karma from previous lifetimes (when perhaps the victim and murderer had reverse rolls). So when people say only God can judge, they mean only God has all the information about these individual souls to know where they stand in their personal moral development.
If we judge based on appearances, we fall victim to Maya, and lose our perception of the perfection of the 'cosmic dance'. If we instead try to further our understanding of these individuals and their motivation we all can grow.
As soon as we 'realize' the perfection of everything, the sooner our own actions will align with the perfect plan, and the more 'perfect' we become. So perfection is a matter of realization of truth. Only our perceptions are imperfect (any biologist/scientist will confirm this).