There's a previous thread on this from 3 years back.
One scientific criticism is the discussion of level of inheritance but he was writing before Mendel's work was rediscovered so he obviously can't have known about genes as unit of inheritance.
In libcom library there's Gould's "kropotkin was no crackpot" essay - Gould feels that Kropotkin was essentially right; that co-operation occurs as much, if not moreso, than competition in nature, especially in harsh or isolated environments.
I'll post the links in a minute.
Also, geneticist Steve Jones revisted Kropotkin in a chapter of his "Coral" book last year - there's a thread where I tried to start a discussion of that but it ventured off into the infamous sociobiology thread instead 



I was wondering if anyone could suggest reading material related to Kropotkin's Mutual Aid. I've okay in terms of the political aspects of it, how it fits into communist-anarchism as well as how others have misrepresented it. I was wondering if anyone could suggest some resources on how it has stood the test of time in biology/evolutionary circles? What are the main objections to it from the mainstream scientific position? Has there been any work on this subject recently?
Many thanks!