Any of these, really. It takes incredible strength to recognize flaws in your entire way of thinking, but if anyone can do it, the Rationalists ought to be able to.
What I'd really love is a link to someone smart saying "This is why I think the Less Wrong people are all misled, and here are good reasons why." But that's probably too much to expect, even around here.
Okay. This may not be the kind of thing you had in mind, but the way I personally think about things:
is probably not focused enough on emotions. I'm not very good at dealing with emotions, either myself or other people's, and I imagine that someone who was better would have very different thoughts about how to deal with people both on the small scale (e.g. interpersonal relationships) and on the large scale (e.g. politics).
may overestimate the value of individuals (e.g. in their capacity to affect the world) relative to organizations.
The way this ...
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.