Fixing the mess is at least straightforward. Discard software patents. Their legality has always been questionable, for sound technical and legal reasons, and they're one of the greatest drains on the patent office. They also have profound, demonstrable adverse effects on industry and on innovation in practice.
Is it really? Now suppose that instead of that clever new valve the OP was talking about I invent a whole new concept of fuel injection that also saves 5% of fuel. And I have an implementation, but as software in a standard electronic fuel controller. Do I deserve a patent? If not, why is it fair that the OP gets rewarded for his mechanical invention, and I am not for my software invention?