I've heard this speculation before, and I'm not doubting it, but I feel that the first part of Genesis 6 is rather obscure, and could mean any number of things, including God chose Noah because he was righteous.
Ok, here's something else to think about. God made two individuals. Obviously humanity had to come from these two, and then from their children. Adam and Eve would have had to of been quite different genetically in order for their children's children not to have problems. If this is the case then, God must have created genetic diversity into the human race as a way to avoid problems with the genetics of bother/sister pairings. In this way it still goes against the data, people should still have more genetic diversity.
Another possible idea I just thought of, was that there was no such thing as a recessive trait until the fall of man. Man's gene's were perfect, but became over time more and more imperfect due to exposure to mutagens. Imagine the possible amount of muation a germ line could take up when the people were living 900+ years. This could possibly help explain the genetic diversity we see with the chimps..
Here's where I have a problem with Evolution... where is the evidence of mutagenic speciation? Let alone randomly mutagenic evolution?
Why? You think if he was such an all powerful being, he could make DNA that didn't have sibling problems. You make him sound like a hacker banging out a quick and dirty work around to a bad initial design.