My biology is pretty terrible, but I'd argue that it takes more than just one or two generations to permanently change the genetic makeup of a population.

To be more precise: I know there are animal species that changed their natural colors to grey-ish tones nearby the cities in less than 100 years, but that seems to me more a result of selective breeding: the non-grey individuals were eaten/killed, so in a relatively short span only those with the grey gene survived. However, given that we are not killing those that are born without the obesity gene, there shouldn't be any reason for such change at a genetic level in such a short timespan at a big scale (unless the obese were over-breeding the non-obese by at least one order of magnitude, which is nonsense).