In this discussion, we have at least two themes:
-->first, what Quillen and Webster put forward in two papers (Q1 and Q2), with Wagner having adopted the 97% grant rate of Q1 and Lemley and Moore (and others) having adopted the 85% number of Q2.
-->second, what Wagner is proposing to do with a quality index in the context of the cooperative venture among open source people, IBM (and others), and the USPTO.
Of the first issue, I agree with your points that the claims define the invention (which is missed in both Q1 and Q2) and that the number of unchanged claims in the prosecution of applications is less than 50%. Discussion of this number came out in the Festo case, wherein the parties discussed the scope of the impact of the absolute bar. Additionally, the presumption that the patent grant rate is an indicator of patent quality can be questioned. Looking only at grant rate does not address the scope of the allowed claims, which can be distinct from the scope of the submitted claims. In the final report by the National Academy of Sciences, the panel did not rely on the numbers of Quillen and Webster, but did rely on a perceived higher grant rate in the US relative to Japan and Europe to infer the presence of a patent quality issue in the United States. The NAS panel did not contemplate the impact of different rules among the US, Japan and Europe.
The patent quality issue served as common ground to involve many players dissatisfied with the patent system to get traction for patent reform, in the body of HR 2795. However, disagreement over the injunction issue among major players killed off 2795. Of course, 2795 was disconnected from the fee diversion issue, which also went nowhere. In the end, the USPTO pretty much ended up where it started.
Enter the open source initiative. Here, the PTO gets access to "free" resources to aid in the evaluation of a problematic area. Not a problem. But tacked on is a lingering vestige of the quality discussion, spearheaded by someone who thinks the PTO grants patents on 97% of all applications. In one irony, using the proposed metrics (including re-exam and litigation success), the Eolas patent, a poster child of evil to many in open source, will look like a high quality patent. [As an aside, note that the re-exam of the Eolas patent which has now concluded was initiated by the USPTO director (with a strong push by W3C), and not by Microsoft; we now apparently have a different re-exam.] In another irony, the quality examination initiative proposed by Wagner appears to fall within the scope of an issued, in-force US patent. If the open source folks use a patented approach to evaluate patents, doesn't that undercut their underlying claim to fame a bit?