In my opinion, part of the “Alice” patent problem is that few true impartial (i.e. neutral) judges have really been involved yet.
Both the USPTO and Federal judges have at least a subconscious incentive to get complex patents off of their respective desks with a minimum of time and effort. Why fill your head with complex matters — just say the patent is “abstract”, and the problem is gone. Instant relief! So perhaps there is an inherent conflict of interest built into the legal system in this regard.
So, as the Supreme Court itself warned, Alice will continue to swallow up more and more patent law until it finally reaches an opposing force. Given our legal system, this opposing force may have to be formed by group of middle to large sized companies. Here, any company that doesn’t depend on either advertising, copyrights, or non-innovative technology might be a potential candidate for such a group.
Perhaps some of the presently pending cases will eventually put some boundaries here.