I wonder if things would have gone differently if the American Pliestocene megafauna had survived. Some of them might have been domesticable, which would give the Americans large domestic animals to work with and animal-origin diseases of their own - which might not really help them directly (they'd be immune to their own diseases not Europeans), but would mean when the first explorers go back to Europe in the 1500s it's Black Death II time. I remember from reading Charles Mann's
1491 that there are estimates that as much as 95% of the population in parts of the Americas might have been killed off by the epidemics, imagine that happening in Eurasia at the same time... I guess that might actually help the Americans, as while the epidemics were burning their way across the Americans the Europeans would probably be a bit busy having their own equivalent apocalypse to do much conquering.
Man, that would be a kind of interesting (but pretty dark) timeline...