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The biggest problem in American prisons is the advocacy by law enforcement of inmate-on-inmate rape as a sanctioned form of punishmentDo you know if this is correlated with overcrowding of prisons (actual capacity vs. intended capacity)? You mentioned California prisons are some of the worst, to my knowledge they are also the most overcrowded?
What strikes me in a comparative analysis of the US penal system is not quality of treatment, but the perverse economic incentives promoting hoarding such a large percentage of the population in them. I would argue the biggest problem in the American penal system is public policy structuring unrehabilitated prisoners as assets:
1a. The standard contract for private prisons seems to be money per prisoner housed rather than money per prisoner rehabilitated.
1b. Each prisoner generates further revenue for the private prison as a labor source.
1c. Thus on a balance sheet, each additional unrehabilitated prisoner becomes an asset to be kept rather than a liability to be reduced.
2. Allowing drugs inside prisons becomes an efficiency gain, as prisoners failing drug tests results in assets being held longer.
3a. When prisoners are housed in prisons in rural districts, they count towards that districts population for purposes of calculating representation in state legislature. Even though prisoners cannot vote and are primarily from urban districts.
3b. Prisoners then also become an asset rather than liabilities for politicians in rural districts by giving them undue representative power. Politicians then are incentivized to increase this asset by supporting minimum sentencing laws.
Now there may be no direct agency or conscious intent to the above, but historically changing the underlying structure of economic incentives can have profound positive effects on individual behavior: http://www.npr.org/blogs/money/2010/09/09/129757852/pop-quiz... . I'd be interested to know if this perspective fits with your knowledge of the subject.