When reinvention is too common, and converging solutions to a given problem can be readily devised, it's not a patentable idea by the constraint of "non-obviousness". But such patent applications readily get granted still. That does not mean the concept (including non-obviousness requirement) is flawed. I agree that it may be impractical given that non-obviousness is not measurable.
The duration of the patent in my terminology is also an implementation issue and not a conceptual issue. I agree that in today's world, twenty years are a bit too long. Or rather inventions that can be so readily made should be failed on "non-obviousness" basis again.
The real issue is this: Not the patent system, but the companies are interested in protecting "everything" they do. The law does not provide protection for everything. Copyright applies to specific material or implementations while patents apply when those three constraints are met. There are clearly things that are not protected by either and they should remain as such. The issue is that they don't (and both companies and patents office are responsible for this).
To fix (the implementation), the bar on non-obviousness, novelty, etc. as well as the duration of the patent needs to be made commensurate with the reality, taking into account the low investment costs and timeline that you mention. Maybe even by having varied durations for different domains just as the non-obviousness bar is different for different domains just by virtue of being unmeasurable.
All in all, I have not heard any real reason why software patents should be distinguished from other patents, other than possibly having the bar on them and duration adjusted accordingly.
Edit: Disclaimer: I am not a lawyer.