I personally don't think the answer lies in abolishing patents because I don't think there is or likely ever will be sufficient impetus behind such an effort to make it happen. There is more hope someday of doing away with software patents but this will take many years given the recent Bilski ruling and Congressional inertia.
I don't pretend to have an answer to this. I suspect that, long term, there needs to be a severe curtailment of software patents, if not an outright abolition, in order to bring the system in line with what it used to be 20+ years ago. I have represented innovators for decades. In the past, I used to tell them: don't copy someone else's code unless you have a right to, watch out about misusing a former employer's IP, etc. and you will be fine. Today, I can't do that. Anyone can wind up infringing all sorts of nebulous patents at any time simply by doing completely independent and innovative work using nothing but one's own skills, knowledge, and talents. That is a very sorry place to be, and it has to change but how and when - that is what is so very frustrating. The author of this piece has the right sense of things but he, like me, winds up at the end basically howling at the moon in frustration over the utterly dispiriting short-term course of events.