I'm not sure what you are exactly proposing with your suggestion to "patch the argument". Here is my understanding (possibly incorrect, I've not been here for long) of what happened:
Yudkowsky claims to have found a practically usable method of inductive inference that is superior to the mainstream scientific method. In order to demonstrate it, he picks an area where mainstream scientific epistemology failed to yield conclusive and satisfactiory results: the interpretation of quantum mechanics.
Armed with his superior epistemology, he sets forward to shine the light of reason on the darkness of chaos and confusion and... fails spectacularly.
So what do you make of it?
1) Yudkowsky's epistemology is not as good as he claims
2) The issue is very technical and Yudkowsky's lack of domain expertise prevents him from making an informed contribution
3) Both
If you pick 1) then you may want to "patch" the epistemology, but that doesn't seem an easy task. In fact, it would be far from obvious that it could be even patched rather than just be discarded as a failed attempt.
If you pick 2) then you may want to "patch" the domain expertise and see whether the Yudkowskian epistemology leads to a better result, but that requires said epistemology to be defined well enough that it can be uncontroversially applied by people who are not Yudkowsky.
If you pick 3) then, well, good luck.
fails spectacularly
This is too harsh. Yudkowsky's conclusions aren't that far from the positions of many mainstream specialists. The main problem with the sequence is, as Mitchell_Porter has noted, its overconfidence and insistence on obvious superiority of MWI. But that is a rather subtle mistake; calling it a spectacular failure would be needless exaggeration.
Also, I think the E.Y.'s epistemology is sound (and not that exotic; most components have been around for decades at least) and his expertise (or lack thereof) may have caused him to overlook som...
This article should really be called "Patching the argumentative flaw in the Sequences created by the Quantum Physics Sequence".
There's only one big thing wrong with that Sequence: the central factual claim is wrong. I don't mean the claim that the Many Worlds interpretation is correct; I mean the claim that the Many Worlds interpretation is obviously correct. I don't agree with the ontological claim either, but I especially don't agree with the epistemological claim. It's a strawman which reduces the quantum debate to Everett versus Bohr - well, it's not really Bohr, since Bohr didn't believe wavefunctions were physical entities. Everett versus Collapse, then.
I've complained about this from the beginning, simply because I've also studied the topic and profoundly disagree with Eliezer's assessment. What I would like to see discussed on this occasion is not the physics, but rather how to patch the arguments in the Sequences that depend on this wrong sub-argument. To my eyes, this is a highly visible flaw, but it's not a deep one. It's a detail, a bug. Surely it affects nothing of substance.
However, before I proceed, I'd better back up my criticism. So: consider the existence of single-world retrocausal interpretations of quantum mechanics, such as John Cramer's transactional interpretation, which is descended from Wheeler-Feynman absorber theory. There are no superpositions, only causal chains running forward in time and backward in time. The calculus of complex-valued probability amplitudes is supposed to arise from this.
The existence of the retrocausal tradition already shows that the debate has been represented incorrectly; it should at least be Everett versus Bohr versus Cramer. I would also argue that when you look at the details, many-worlds has no discernible edge over single-world retrocausality:
I am not especially an advocate of retrocausal interpretations. They are among the possibilities; they deserve consideration and they get it. Retrocausality may or may not be an element of the real explanation of why quantum mechanics works. Progress towards the discovery of the truth requires exploration on many fronts, that's happening, we'll get there eventually. I have focused on retrocausal interpretations here just because they offer the clearest evidence that the big picture offered by the Sequence is wrong.
It's hopeless to suggest rewriting the Sequence, I don't think that would be a good use of anyone's time. But what I would like to have, is a clear idea of the role that "the winner is ... Many Worlds!" plays in the overall flow of argument, in the great meta-sequence that is Less Wrong's foundational text; and I would also like to have a clear idea of how to patch the argument, so that it routes around this flaw.
In the wiki, it states that "Cleaning up the old confusion about QM is used to introduce basic issues in rationality (such as the technical version of Occam's Razor), epistemology, reductionism, naturalism, and philosophy of science." So there we have it - a synopsis of the function that this Sequence is supposed to perform. Perhaps we need a working group that will identify each of the individual arguments, and come up with a substitute for each one.