I have read CLS v. Alice a half a dozen times. I have read the follow-up cases, including Ultramercial v. Hulu (holding software patentable, opinion by Judge Rader) and its counterpart Accenture v. Guidewire (holding software as unpatentably abstract, opinion by Judge Lourie).
Greg Aharonian of the Internet Patent News Service collected some quotes from the judges in CLS v. Alice.
the patent-eligibility test has proven quite difficult to apply
the current interpretation of 101 is causing a free fall in the patent system
our court is irreconcilably fractured
we have propounded at least three incompatible standards, devoid of consensus, serving simply to add to the unreliability and cost of the system of patents as an incentive for innovation
the intervening commotion [since Diehr and other decisions] leaves us with little, if any, agreement amongst us even though the statute as not changed a syllable
Chief Judge Rader
[o]ur opinions spend page after page revisiting out cases and those of the Supreme Court, and still we continue to disagree vigorously over what is or is not patentable subject matter
courts could avoid the swamp of verbiage that is 101 by exercising their inherent power to control the processes of litigation [by focusing on 102, 103 and 112]
Based on this, and the opinions, I have come to two conclusions. First, the Court of Appeals for the Federal Circuit is just as confused as I am about software patent eligibility. Second, the panel members you draw on the CAFC will determine whether a software patent will be upheld as valid or struck down as abstract. If you draw Judge Newman, Rader, Linn, and O’Malley, the software patent will live. If you draw Judge Dyk, Prost, and Reyna software is clearly abstract.