Go the link, go to references, read about them. I'll outline the gist: Most of what Yudkowsky says is extremely sci-fi, no real basis in scientific fact, but stretching the current technological progress to the point where his opinions on things (stuff like transhumanism, singularity) can be justified.
What he's preaching isn't science. Certainly not rigorous experimental science. He (along with Bostrom) tends to engage in extreme hypotheticals. Which, sure if you're a philosopher, is fine. But even then, wouldn't you want your work to be judged by like-minded peers? But alas, here has a convenient excuse of being "auto didactic" to fall back on, so he can sit on his armchair and critique traditional education, and his lack of peer reviewed material.
Not to mention, and this is a bit of a pet peeve, I find that most LW people are too self-absorbed, I've literally seen a blog where the person who runs it "warns" the readers that what he writes is too complicated for people to follow. This sort of narcissistic, self congratulatory thinking is what puts me off more than anything. Writing long form posts on the Internet which use complicated words don't make you smart.
http://laurencetennant.com/bonds/cultofbayes.html is another critique. It comes off as bit crass, but stick with it.
> I've found LW a tremendously rich source of thinking tools and I'm convinced that reading or skimming a lot of the sequences have improved my thinking.
There are other ways to improve your thinking. Read books. Read different kind of books, that offer counter point of views. Farnham Street Blog is a good place to start for a list of resources for thinking tools/mental models btw. :)