The Ars Technica piece is very slanted, pulling quotes our of context. Here's the full text of the speech itself: http://www.uspto.gov/news/speeches/2012/kappos_CAP.jsp
For instance, compare these quotes, which give a very different perspective:
"But it is equally important that patent protection be properly tailored in scope, so that programmers can write code and engineers can design devices without fear of unfounded accusations of infringement. And we know that inconsistency in software patent issuance causes uncertainty in the marketplace and can cause threats of litigation that in turn can stifle innovation and deter new market entrants."
"Software experts have long observed that programming is incremental in nature, with modest improvements not worthy of patent protection. KSR gave us the ability to recognize this valid observation and incorporate it in our examination process."
"Should we just accept the problems, given the importance of the innovation and the illogic of discriminating against great technology that happens to be implemented in software? Of course not. The right point of inquiry is quality. By getting that right, we grant patents only for great algorithmic ideas worthy of protection, and not for everything else. This administration and its innovation agency understand that low-quality patents do no good for anyone. Low quality patents lead to disputes, uncertainty, and lost opportunity. Quality is central to our mission. All of this especially for software."
"One such initiative has already begun crowdsourcing searches for software prior art. It's called Ask Patents and is an online network hosted by Stack Exchange, where software experts engage in robust discussions of possible prior art for given applications, then submit the best prior art along with helpful commentary."
"You know, the history of software patents is not a perfect one, although things are improving. Some of the most troublesome patents have expired; others can be challenged with new post-grant proceedings; and newer patents are quantifiably clearer, and aligned with current legal standards."
"For those who feel more needs to be done, we encourage you to keep reaching out to us at the USPTO, as well as to other actors who also have an important role to play. The USPTO administers the laws, while Congress and the courts write the laws and interpret them, respectively. Working together, we can find the right balance for software patents. We can find a balance that ensures market certainty, encourages investment and research and product development, and guarantees that patents issued going forward are appropriately tailored."