It seems to me that paleoanthropology is adding new bits of information that may very well challenge some of Diamond's presuppositions. I can think of two examples off-hand. One denies an "out of Africa" population genesis because core samples show massive drought during the theorized exodus period. Another posits an out of India exodus instead of an out of Africa exodus. These and other mounting bits of data may or may not contradict or confirm some of Diamond's essential presuppositions.
I actually think that Diamond's argument in Guns, Germs, and Steel is best read alongside his next widely-read book Collapse. He shows in the second book how human culture, and particularly human decisions, affect their success or failure. This is a sort of fleshing-out from GGS, in which he comes close to arguing for complete environmental determinism.
I have a hard time thinking of anything to disagree with in this book. I agree with Diamond's entire argument. I think that the "natural experiment of history" from Chapter 2 is one of the most compelling arguments in the book. It seems to prove without doubt that (at least in this case) it was environmental factors that caused one group to dominate another, not ethnicity or culture.