It's the null hypothesis. For me personally, it's more a bet against the modern microbiome than it is a bet for the ancestral one.
See also paleo vs margarine, no fat, no cholesterol, no carbs, enough poly-saturated fat, enough omega 3. Really paleo vs any nutrition advice that's more than 10 years old (so the science had a chance to check the claims)
IMO we don't currently know enough about nutrition or the microbiome to make a better choice than "whatever our great-great-great grandparents did"
> Do you think they all had the same microbiome?
They didn't, but they had way more diversity and significantly different strains than moderns do. Check out my above link to the american gut project's founder or http://journals.plos.org/plosone/article?id=10.1371/journal....