Eventhough I don't agree with your first sentence for problem 1, I agree with you totally. I just have to say that fish do not have incest taboo like people (well most people). Wild or not, a male will breed to the nearest female in any situations.

Problem 3 is ideal, but it will never happen.
The market for boats will be ruined if the rivers were to be put back to its natural state. Moreover, liability issues from boaters will be sky high.

Bossman, that was an unfair comparison.
The Western WA rivers are not as drastically different as Alaska to Africa.
If you believe much in evolution and the survival of the fittest through natural selections, the small changes b/w Western WA river may bring out stronger generations of fish.

I believe in the near future when DNA collection and analysis are better and cheaper, the hatcheries will be able to use DNA to document and to select breeders according to their genetics.