"The patent system's primary goal seems to have become protecting patent holders, which really ought to be only a secondary function. The original purpose of patents was to encourage innovations that would benefit society. It was a simple trade: if you invent something that will help society, society will give you protection against competition for some period of time."

Exactly. How do you have one without the other? Should Microsoft (or any other patent holder) go to court and argue on the basis that society is not being well served?

The patent owner needs to show harm, which is what patent law was supposed to protect them from. The stated reason for such laws is "to promote the progress of science and useful arts", but if you are a patent or copyright holder your argument needs to be that you are not being provided the protection you had expected under the law.

"And in the case of software patents like the ones in this suit, society receives very little benefit for the protection it provides."

That may be. Some patents are for essentially trivial ideas, or ideas that have been in the ether for quite some time. Other patents are indeed clever, and more to the point are the results of an investment of time and money. Without some assurance of recouping that investment some number of valuable ideas would not see the light of day. (Or so I believe. I don't have any citations to back this up.)

Any article that simply refers to a patent abstract as proof of the triviality of a patent is itself trolling. Patent abstracts offer a very broad description; it is the detailed body of the patent that distinguishes it.