The availability of suitable species for domestication always struck me as the most interesting part of his argument, as it's not one I'd seen before - but strangely it's the one that's not captured by the title "Guns, Germs & Steel" (which are, I suppose, the main proximate reasons why Europeans ended up decimating/overpowering populations elsewhere in the world, rather than more interesting fundamental reasons why Europeans got to the point they could travel the world possessing said items well before any other candidate civilizations did. Accepted, "germs" is related to ability to domesticate various animals, but hardly captures the full set of advantages that came from animal and crop domestication).
I never thought his explanations of why it couldn't have been China or India instead were that compelling though, not does he bother to explain why certain European nations became far more successful as colonial powers than others (e.g. why were Germany and Italy so late to the game, and unable to really compete with Spain/the Netherlands/Great Britain as far as colonisation efforts went).
Hence demonstrating there was at least one other key factor behind which nations/empires were able to successfully establish overseas colonies - but arguably that itself was not an "ultimate" cause that was out of the control of earlier civilizations (in the way availability of species suitable for domestication was). If the Roman empire hadn't collapsed the way it did the world would surely look very different to how it does today (I wouldn't be writing this in English for a start!). I don't think that's something Diamond addressed in GG&S, and even in Collapse I don't remember any serious discussion of how it might be ultimately and primarily due to geo-environmental factors (for a start, the empires that replaced it over the following centuries were operating in very similar ecologies/climates). I don't think Diamond would insist that the pattern of historical development of specific nation states was largely due to the ultimate causes he tries to identify for overall European hegemony, but it would be surely worth clarifying at what scales other factors start to become more important (and what those factors might be).
(Actually the far better example is France - in principle, at the time, it was better obviously placed to achieve colonial domination than Spain or The Netherlands or even Great Britain. The argument seems to be that it was too focused on waging wars within Europe itself to commit itself to overseas exploration etc. But is that an "ultimate", proximate or some sort of intermediate cause?)
