The Problem with Christians

[AAA]

What it really seems to boil down to is that because the universe is not perfect, there is no designer? Is that a fair summary of your point? 

Not even slightly. In fact, I have to assume that you deliberately missed the point of what I said, that's how horrendously inaccurate your summary is. The universe is not perfect, therefore the designer is either imperfect itself or created a flawed system on purpose, ergo this designer is either a capricious god or no god at all. 

Also I like I said before, the same laws of chemistry that enable life as we know it to exist also allow molecules to unfavorably interact with DNA to damage it. 

Some design.

Maybe the fact that biological systems are damageable is a sign that we are becoming genetically weaker as a biosphere, which points to the idea that it was once superior in the past. It indicates that we are declining rather than improving.

Some. Design.

Yes I exaggerated your point on purpose, but I think it is essentially what you are doing. The design is pretty much as good as it can get. Some enzymes are actually kinetically perfect, meaning they catabolize reactions as fast as they encounter substrates. There are mechanisms to prevent cancer. I suspect that the reason that genetic diseases occur (i.e. they are not all fixed by DNA repair enzymes) is because having excessive mechanisms to avoid DNA damage would eventually become too energetically costly to the cell. In other words, there is probably a threshold where it would require too much energy (which would decrease the organism's quality of life) in order to manufacture enzymes to prevent all genetic disorders (which also decrease the organism's quality of life). 

In other words, things are optimally designed. You have constraints because improving one aspect impairs the function of another. An easy example to grasp is axon diameter. The larger the axon, the faster the signal. Why not have all axons be 20 cm wide? Because it would cause crowding which would impair the functioning of neighboring cells. Does that make sense?