I don't think the idea of patents is flawed. They work well in certain industries (namely pharmaceuticals). The problem is that the patent system was never designed to cover intangible goods. The idea that one single device can simultaneously infringe tens of thousands of separate patents is an abomination.

That leaves the problem of how to exclude software from patentability without causing problems for Pfizer and General Electric, but I think that's coming at it from the wrong end. Never mind what you can get a patent to cover or not, just make intangible goods incapable of patent infringement. Pass a law that says that if all you're doing is distributing bits or executing a program on a general purpose computer, you can't be liable for patent infringement whatsoever. That should have no effect on the makers of cholesterol medication and jet turbines while solving the problem for software developers.