And also recall with patents you are guaranteed another appeal to a different body if ever sued, the courts, where you can invalidate a patent. And if MS wins the i4i case the burden of proof will be even lower. And note, there is legislation going through congress right now to make it harder to win a suit, and also expands patent reexamination.
My point? The patent examiner is an important first step, but a patent that clearly has no legs should be defeatable -- if not now, in the near future.
The conclusion that you should be reaching is software patents are simply not a viable mechanism, period. In other words, even if you like the idea of patents in theory, in practice they do not work because we will never have enough patent examiners with the necessary expertise much less time to make valid decisions on patent applications.