The supposed growth from 29% to 60% has been entirely due to the America Invents Act, which requires a new treatment of patent litigation. Under the old rules, NPE's could sue a boatload of defendants in one litigation. Under the AIA, NPE's had to file unrelated defendants separately. The net result is that NPE's have to file more suits for the same number of defendants.
Another point of interest not discussed in the NYT article is that lawsuits by others (non-NPEs) dropped in total numbers in 2012. Indeed, excluding NPE's, the number of patent lawsuits per year has remained fairly constant, which should be a surprise given that the total number of patents issued by the USPTO has continued to rise.