I have recently read an interesting 2006 post from Steve Yegge titled Good Agile, Bad Agile. The comments section has also informative criticisms.
It's good to read and understand various ideas. From my experience and knowledge so far, I think the biggest problem with methodologies is that company X can be so different and it is very easy to blindly 'adopt' a methodology without putting in the effort in understanding it. The same with religion and superstition. (Idea I got from this article).
The most interesting idea I have learned so far on this topic however comes from Edgar Schein. Paraphrasing the idea: "Professional Relationship hurts Communication". I highly recommend listening to him on YouTube. I look forward to read his books.