4.There is no "patent litigation crisis", just increased media coverage of litigation that is more or less in line with historical rates.
From reading that paper, the raw numbers look bleak to me - pretty much all of them doubling over the last 10 years. My only hope is that the AIA is actually causing the inflation in patent lawsuits the paper claims. There does seem to be some evidence in it that it is.
I also don't find looking at percent of patents in force very useful. Even if that number remains flat, the number of patents in force increases. What I'm interested in is how many businesses are getting screwed over. If that percent remains flat but we had a huge upswing in patents granted it would be tragic, and it would be hidden behind the 2% number that doesn't really matter.
Also, "historic rates" goes back to 1923. The software sector has not existed for nearly that long, and making comparisons to a very different economy doesn't seem that useful.
The numbers may be bleak when viewed in isolation, but taken as a percentage of all active patents, the number of patents asserted in lawsuits have been remarkably constant. The more recent spike, as you surmised, can be attributed to the AIA joinder rules.
You may worry that the spike in number of active patents is unhealthy, but again, there are studies that indicate that this is due to increased innovation than just over-patenting: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=556630
As for number of patents getting "screwed over", that is a very difficult metric to measure, simply because "screwed over" is ill-defined. If you can define "screwed over" I might be able to find a paper that tries to measure that. (Seriously, SSRN appears to a number of papers on all kinds of crazy topics.)
The Katznelson paper is not about just software and patents. By "historic" rates, the paper means revolutions in technology similar to those wrought by the computer revolution. Similar litigation rates have been observed in the past when major new technologies were introduced, such as radio and microelectronics. They are not the same thing technically, but the potential for new applications that these new technologies introduced is similar.
From reading that paper, the raw numbers look bleak to me - pretty much all of them doubling over the last 10 years. My only hope is that the AIA is actually causing the inflation in patent lawsuits the paper claims. There does seem to be some evidence in it that it is.
I also don't find looking at percent of patents in force very useful. Even if that number remains flat, the number of patents in force increases. What I'm interested in is how many businesses are getting screwed over. If that percent remains flat but we had a huge upswing in patents granted it would be tragic, and it would be hidden behind the 2% number that doesn't really matter.
Also, "historic rates" goes back to 1923. The software sector has not existed for nearly that long, and making comparisons to a very different economy doesn't seem that useful.