Patents fundamentally operate to allow the owner of protection to extract value from research and development investment. If you cannot protect your research and development, then competitor may extend upon your invention without the necessary capital or time investment — effectively making any kind of innovation risky and unattractive to business. There is no model where abolishing patents still grants protection for R&D.
The complaint is that software patents have been awarded and interpreted far too broadly, and coupled with the relatively low cost of R&D for software, have begun to stymied innovation in the same way patents intended to prevent.