This is all new stuff, and not like it's been enshrined in law forever. Software's only been patentable for ~40 years, and it coincides with the greater influence of business on politics. IOW, the laws are bought.
And just how long has software been around? Not much longer than 40 years.
The fact that a technology is "new" does not render it patent ineligible. The cotton gin was "new" in the 1700's, yet was considered patent eligible subject matter.
The wheel was "new" at one time too, and yet is still patent eligible subject matter. Hell, one of my former clients was a huge tire (wheel) manufacturer. There are lots of patents covering tires.
Again, note that I am using "patent eligible" in contradistinction to "patentable." They mean completely different things.
Most importantly, it goes against the purpose of patents. The purpose is to spur innovation. Awarding the inventor a monopoly is a means to an end, not the end itself. Software patents retard innovation, and build a climate of fear which holds back development. It also needlessly increases cost as businesses buy up patents to use as defensive weapons, and litigate nonsense in court, or not as the case may be. Many times it's just cheaper to pay off the adversary, and pass the costs on to the customer.
You, like many people who are not well informed with respect to U.S. patents, are mistaking the trees for the forest. True, there are some entities (e.g., patent trolls) who purposefully buy patent portfolios for the express purpose of extracting revenue in the form of license fees, while not actually practicing the inventions claimed by the patents in the portfolio. Those entities are not the majority of patent owners, or even a substantial percentage of them. They just happen to be the most well known because the public often disapproves of their actions, making them media worthy.
Even still, it is not clear to me why the actions of a patent troll are "wrong" given the framework of the patent law, which is structured to create limited and temporary property rights in the subject matter claimed in in a granted patent. In this way the claims of a patent are similar to real property (i.e. land), in that the owner has the right to exclude others from the property. No one would say that an owner of land was wrong for ousting a trespasser, even if the owner was not presently using the land or even if the owner had never set foot on the land. So why is it so outrageous that a patent troll acts in the same manner, i.e., to exercise his exclusionary rights over technology claimed in a patent, even if he/she is not using that technology?
Second, your arguments that software based patents stifle innovation is narrow minded and misses a key point. One of the primary ways that patents foster innovation is by encouraging businesses to design around patent claims. This encourages full exploration of a problem and the production of myriad solutions to that problem. The fact that some solutions may be less efficient and/or effective does not take away from the fact that their development advanced the useful arts with respect to that problem.
As to your comments re: cost - I again encourage you and everyone else interested in this topic to read up on the america invents act. Among other things, the AIA introduces myriad ways to challenge an issued patent without having to resort to full blown litigation.
Also, you may be interested to know that Congress is presently voting on a bill that is aimed to address the patent troll "problem." I have not read the bill under consideration fully yet, but my understanding is that it would give judges more authority to levy sanctions on litigants that bring patent suits that are not meritorious, and would require more detailed pleadings for patent suits. The latter raises the barrier to entry for patent trolls wishing to file myriad suits, and the former provides a sword with which a judge may punish a patent troll who makes it into court (i.e., files a suitable pleading) but whose claims ultimately prove to have no merit.
Finally, to the extent your arguments stem from your general dissatisfaction as to the breadth of some patents that are issued by the USPTO - the proper way to correct that issue is to reconsider those patents and find them to either lack novelty under 35 U.S.C. 102 or to find them obvious under 35 U.S.C. 103. It is not to find them patent-ineligible under 35 U.S.C. 101, which is the issue in the CLS case that is going to the SCOTUS.