I was at the CAP event this morning, and I wouldn't say the Ars story is that slanted. Did Kappos say that there is absolutely no improvement to be made to the US patent system? No. Are there some positive things going on at the patent office? Yes. However, he frankly came off as a total hack. Here is why:
He led off with a statistic about how "IP intensive industries" account for 40 million jobs, and 35% of GDP. Even if you accept the methodology behind those numbers, the vast majority of the jobs and GDP come from trademark intensive industries (e.g., retail) rather than patent intensive industries (or copyright). I called him on this in the Q&A, and he gave a politician's response (e.g., a non-answer).
He kept mentioning how "critics" don't have the "facts" but failed to even once suggest why high-profile innovative companies like Google are critical of software patents.
He claims that "Our founding fathers enshrined patent rights in our Constitution, an affirmative right here, that in other countries is only issued grudgingly. It’s one of the few, if not only, clauses in the Constitution that gives Congress the right to create personal property." This is inaccurate. The Constitution mentions that Congress has the power to secure to inventors their discoveries for limited times. It does not say that this must be done through patents, and it certainly does not analogize whatever method Congress chooses to property.
He claimed that "our IP system is the envy of the world." Well, I've actually talked to European Commission officials about what they think of our patent system, and they don't share his view. Actually, much of the world doesn't want our ultra-strong IP laws. Maybe he meant to say our "economy" is the envy of the world (although that's also a hard sell). He also seemed to think that our system was best because it was strongest... shockingly, I think there are a lot of people who don't think that strongest = best, yet he doesn't address this.
Essentially the bulk of his logic boils down to a post hoc, ergo propter hoc fallacy: The U.S. has software patents, the U.S. has software innovation, therefore the software innovation must come from the software patents. This is logically false, and I would also argue empirically false.