It makes me wonder if our relatively little diversity is related to the uncanny valley and our ancestors eliminated any variation that wasn't enough like themselves.
The human response to diversity seems to be "KILL KILL KILL" unless mental effort is employed to override this natural response. I've wondered for a long time if there are no other hominids, and so little diversity in our own species, because we killed them all. Genocide seems to be in our natural emotional structure.
But I wonder if this could be related back to the bottleneck. During a bottleneck, inbreeding-related genetic disorders become an issue. Maybe evolution selects for genetic "purging" behaviors during such bottlenecks as a means of ensuring fitness... basically during the bottleneck you'd become Nazis to escape the effects of inbreeding, and these impulses might stay afterwords.
So your theory is that, to avoid inbreeding, we developed a "KILL KILL KILL" response to differences and diversity. Somehow, I don't think that that makes sense, unless you're thinking of it as a way to get societies to reject people born as a result of inbreeding. Neanderthal predation is a much better explanation, at least in my opinion: a intrinsic fear of things that look very like us but different because, not so long ago, things very similar to us were trying to kill and rape[1] us.
[1] Ellyagg mentions a study that showed that humans have some male neanderthal DNA, but not female neanderthal DNA. This, to me, suggests rape. http://news.ycombinator.com/item?id=2688389
