This really seems to boil down to arguing that the patent examiners in the software art unit need to do a better job evaluating whether patent application claims really are novel and non-obvious, like they're supposed to under current patent law.

For several years they were really overwhelmed as the volume of software patent applications exploded and they couldn't hire well-qualified software patent examiners at nearly the same rate. Traditional patent examining practice of looking primarily at existing patents and secondarily at academic publications to show the state of the art also tended to miss a tremendous amount of publicly known subject matter. The examiners have been getting steadily better and more creative in searching for references though.

Perhaps the rule that catches RSA, but not One-Click, is something like:

"An invention that applies old theory to solve an old problem in a new way."

The idea being that if the problem is long-known, and the theoretical underpinnings of the invention are long-known, yet the invention itself had not been previously described, then it must be novel and non-obvious.

In the One-Click case, the problem itself was new, so only the efflux of time could show if any solutions based on known theory were obvious or not.