In nearly every paragraph of the response, the office manages to imply the petition is misguided and incorrect, implying that the real issue is so-called "overly broad patents", while pointing out the merits of the (insufficient) America Invents Act. There is a paragraph noting that blame also falls onto Congress, and allegedly the Supreme Court as well.
The response also lauds the government's increased use of open source. Perhaps the government will listen when patent trolls arrive on its doorstep, or when foreign interests block the government from using certain types of software or user interfaces, perhaps allowing it with royalties. Until then, there is always https://wwws.whitehouse.gov/petitions#!/petition/actually-take-these-petitions-seriously-instead-just-using-them-excuse-pretend-you-are-listening/grQ9mNkN