it's the patents that are bogus. Judges need to invalidate more patents, they need to invalidate all software patents.
Putting aside the entire issue of software patents, the legal standards for invalidating a patent are rather high. I have seen many patents which we would all likely agree should be invalidated either for obviousness or because there's prior art; but actually meeting the necessary criteria to prove that conclusively to a judge or jury would have been impossible.
It has evolved this way because of the built-in assumption that the Patent Office does its job correctly, and therefore patents are assumed by courts to be valid and there is a fairly heavy burden imposed to prove otherwise. If the assumption is valid, then this isn't an obviously-bad system; but if it isn't valid, then it quickly becomes an expensive, frustrating situation for defendants.