Providing we agree the goal is innovation, it doesn't work as currently practised. A patent is supposed to be an innovation so unique (non-obvious etc) that others are unlikely to come up with the same thing for quite a period of time that the innovator is given a 20 year monopoly (and ability to seek rent) as a reward for telling the world about the innovation details early. This is supposed to accelerate innovation.

The problem with software patents is that software doesn't work in isolation - things are built on other things, so nothing is really standalone. The other problem is that the patents that are accepted are not actually innovative. If they were then there wouldn't be all these other companies to sue for violating them! (It is standard legal advice to software engineers to never read patents.)

The value of patents is not in innovation - it is in providing grounds to sue others and collect rents from them. This has the net effect of slowing down innovation because it is safer to avoid newer things than be in the court room. It also means that competition is limited because others can't "fairly" compete in the same product space. It is ultimately a tax on doing business with the proceeds going to lawyers and others.