It's commonly supposed that the Supreme Court could void these illegal patents - could dissolve this entire illegal industry - with a swish of their shiny polyester robes. Actually they already tried that, in Flook. Jedi mind tricks, which in the end is all the Court really has, worked about as well on Andrew Jackson.
I think this explains the disappointing result of Bilski. If you are supposed to have a magic power which in reality doesn't exist, make every excuse to avoid using it. You may still be suspected of impotence, but at least the suspicion is not confirmed.
Unfortunately there isn't really a solution to the patent problem that's compatible with the rule of law, mostly because the rule of law was so long ago abandoned for the rule of lawyers. Perhaps Andrew Jackson could round them all up and march them to Oklahoma - or at least, Marshall, Texas.