So the argument here isn't that a patent system is inherently bad; you could have a patent system that provides a net win for society. But over time, entrenched interests will find ways to twist the system to their advantage, at the expense of society at large.

Let's say this is true; how is this different from any government action in the marketplace? From education to finance to healthcare, we're confronted with problems that have may have good theoretical solutions by government, but the reality is that our solutions will eventually devolve to rent-seeking and regulatory capture by powerful entrenched interests. I have yet to hear a good solution to this problem other than severely limiting the ability of the government to interfere with markets in the first place.