Rarely is it the case that anything is truly "total". And if the patent system is squashing 25% of innovation in the software industry, or even 10%, that is a big problem.
Also, it is possible to squash certain kinds of innovators - like startups without tens or hundreds of millions of dollars to spend on patent litigation. While massive corporations can get nailed for a billion or two and hardly notice.
A patent-litigious environment is deadly for startups. And startups are crucial innovators.