Hmm, we do seem to have a few things in common.
Another fundamental misconception is that evolution is a synonym for progress. Most people are shocked and disoriented to learn that not only is "improving the species" not the purpose of evolution, but that evolution really has no purpose at all. By that I mean that it's not directional--there is no forward. When a fish with eyes is trapped in a dark cave, its descendents lose their eyes. They haven't regressed or "devolved", they've simply adapted to a new environment in which eyes are a waste of energy and materials.
When I hear people say that genetic engineering goes against nature, I say that's a good thing. "Nature" is a mindless goalless process, so if something is against nature, then it must be intelligent and driven by a purpose.
The other point you make about the eyeless fish is something I've touched on before. My views on evolution are that it isn't driven by random mutation, but is heavily influenced by the organisms involved. A type of biofeedback mechanism in which the organism adapts its form to become as energy efficient as possible in the environment it finds itself in. Eyes are of no use in an underground cave, so the energy used to develop and maintain them is redirected for other uses. DNA resides in the nucleus of a cell, but when the cell divides it creates a copy of the DNA with RNA. RNA exists in the cytoplasm of the cell and is influenced by by both internal and external factors. It is my belief that over the course of time, environmental factors can cause a species to modify its DNA to adapt to external pressures. This idea is based on some of Lemarck's theories. I call it the theory of eutrophy or atrophy, or use it or loose it.