Congress has still not clarified this question. What should be followed is Supreme Court precedent, i.e. Benson, Flook, Diehr. Theoretically, that's the law until Congress says something different.
The word of the Supreme Court should be actual law, not just theoretical law. It's up to the executive branch to direct the USPTO to follow that law. Patents should be examined consistent with Supreme Court precedent.
If the circuit courts were flouting the judgment of the Supreme Court as blatantly as you allege, how come the Supreme Court hasn't granted certiorari on a suitably iconic case and reiterated its judgment in even clearer terms? It's not like there is any rule that prevents that, a grant of certiorari only requires 4 justices to sign on.
I laid out clearly why I think what I think about Benson, Flook and Diehr in http://ourdoings.com/ourdoings-startup/2011-07-28 and I have yet to see a similar outlay of the arguments for an opposing view.
If I've neglected a question about standards of review, I apologize. Please repeat it.
I'm on my phone at the moment and don't really have the time to write a long article in any case; but in a nutshell I think you are making too many assumptions about the meaning of the SCs words without considering their meaning as legal terms of art.
I wasn't aware of that. However, I suspect that legally, Congress must clarify that before it comes into force as law. But I don't know, the Supreme Court is a funny thing. Good question for a lawyer...
Yes, I suppose Obama could start a push to change software patents, but frankly, there are more important things for him to deal with at the moment.