"Are gripes against software patents 'invalid'?"
Many current authors and commentators (though perhaps not as many patent attorneys) contend that the U.S. Patent and Trademark Office (PTO) is fine at examining patents for mechanical devices and pharmaceuticals, but argue that we need a whole new system for examining software inventions best understood by those under 40. They say that the PTO is not set up to examine software patent applications and, as a result, frequently issues patents on trivial improvements to existing practices. Several such authors and commentators have misinterpreted the outcomes of recent court decisions as confirming these notions, when in fact they debunk them.
There is another point of view. As discussed in this article, although patent examiners are human, and determining whether an innovation is worthy of a patent is a very complex undertaking, when the facts and arguments are scrutinized, the PTO is likely, on balance, doing a pretty good job of examining software patents.