"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.

-Exactly. How do you have one without the other?

If obvious patents are granted, society will be giving it's protection at a net loss. For society there is a cost incurred in enforcing protection as well as an opportunity cost in forbidding competition (assuming you believe competition creates better products). This trade-off could be worth it, but only if if the invention would not have emerged, or would have taken a long time to emerge, without protection.

-Should Microsoft (or any other patent holder) go to court and argue on the basis that society is not being well served?

Absolutely not. They should never have to argue for anyone but themselves in court. Microsoft is just playing the patent game by the rules that exist today. My problem is with a system that is neglecting its purpose. The problem seems to be rooted in patent rules that are massively out of touch with the current state (and pace) of technology.

-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.

You're absolutely right in saying that it's not fair to criticize a patent simply by its abstract. The problem is that often the detailed description in the body of the patent is far too broad. Many patents have less to do with a specific invention and more to do with gaining blanket coverage of a large swath of IP. This is the game that large companies and their patent lawyers are playing. I would argue that a system where "he who has the most lawyers wins" is very counterproductive to invention and innovation.

I will be downmodded that much, that I would see the core of Earth, but I have to say it: "a tool for encouraging innovation into a panicked land grab" was the primary goal. Think: who was the people who created patents young/pour inventors, or elite ones that wanted protection from the hungry ones?

It was known even to them that patents were a tool for controlling innovation to their interests (unnaccessible fees, even to poor people). The point is a "patent" of an "invention" should be a right of a citizen, without additional fees. It's not a product, it's a right within the community!

EDIT: We all want to believe that our founders were truly ingenuous good people. But the truth is, they'll never be.