Every patent is written to cast as wide a net and be as vague and obscure as possible. Software patents are not unique in this regard. I agree that this is a major problem with our patent system.
Intent really doesn't have much to do with this at all. If someone holds a patent and someone else invents the same thing, the second owes royalties to the first regardless of whether it was an independent invention. That's why Bell was so hot to get his patent approved before Gray.
The Bell/Gray story tells us that the patent office has been the source of controversy long before software was even known. If software patents are invalid, we must treat every other patent the same way. I think that's a worthy debate to have. I'm not sure whether patents serve a useful purpose at all today. They are mostly defensive shields now.