1. It isn't all recycled. Ever heard of Alchemy? In order to obtain anything you MUST give something of equal value. The fact that many things give more or less than they obtain shows that everything isn't "recycled" and that much is wasted even among nature.
2. Nothing is perfect because perfect is a label just like evil and good thus the standard is ever changing.
3. The human eye is trash compared to other eyes and it's not really as complicated as people think.
4. The human brain is the same as the human eye. It's not that complicated. Of course the word complicated is like the word perfect. A label we use thats standards are ever changing.

Now for a mind blowing theory. What if this being people beileve in is actually multiple beings? Like a swarm of Gnomes or Lizards that exist on a plane of time so different than our own that they are the tool using race rather than humans, and that they decided to simply fuck around? Or what if it's a terrorist attempt to cause us to kill ourselves so they can come in and take over when we obliterate ourselves? OR maybe it's just a flying invisible hand like in Black and White that messes around with shit and is being controlled by these beings because we are really just one complex video game that they play on a daily basis? Your "supreme being" or "supreme powers" are much to full of holes for everyone to simply accept blindly. Just like other theories.