Why most articles miss the point of patents

Apparently two Boston University academics did some research and said that litigation costs outweigh benefits from patents in most industries other than chemicals and pharmaceuticals. But, I think they may be underestimating the harmfulness of the current system. Currently patent holders are not using patents to make money, but mostly as constituents of a portfolio. Without the portfolio effect, there would be a lot more litigation. Indeed, small companies with a small portfolio get hounded out by large companies. Then there are the patent holding companies with no products, that are giving the large companies (who can be far more boisterous than small ones) a lot of trouble. Why is the situation so bad? Patents were intended as a limited grant of monopoly, so there would be an incentive for inventors to contribute to the public good. The invention becomes public knowledge after the patent expires. All nice and good. Unfortunately, patents have become a very effective tool in limiting use of public knowledge.

1. Everyone from the inventor to patent examiner has an incentive based on number of patents approved. The USPTO is a money making organization, and they don't want to compromise that by insisting on the quality of the patent. Consequently, most patents have questionable novelty in them.
2. Patents are mostly used as detterents as a part of a portfolio. Most of them probably are invalid, but testing that validity is extremely expensive.
3. Small companies, that are usually more innovative, are routinely shut down by large companies using their patent portfolios. Case in point, Vonage vs Verizon.
4. Large companies are terrorized by small patent holders. Case in point, Research in Motion paid $500million to settle a lawsuit based on an invalid patent.
5. Patents are granted for the same period of time, regardless of the useful lifetime of an invention. Drugs can take a long time to develop and have decades on the market. Software takes a few weeks to develop and may be 2 years on the market. But patents in both cases are for 20 years.
6. Patenting other people's common knowledge is easy. All you need to do is to get some common knowledge from another country and patent it. Patents on Basmati rice and turmeric are prime examples.