For one, the amount of refined sugar in our diet exploded recently.

More generally, even if the molecular building blocks didn't change, the way food is prepared industrially and marketed makes us more likely to eat too much of it.

In the country I live in, white flour must legally be mixed with iron. In natural foods, iron is bounds to proteins like hemoglobin or ferritin. Legally mandated iron is just "iron", which means whatever's cheapest, i.e. metallic iron powder. This is known to be poorly absorbed:

https://www.ncbi.nlm.nih.gov/pubmed/15864409

So what happens to the non-absorbed portion? I have read speculation that it could affect intestinal bacteria. Intestinal bacteria are poorly understood, but widely believed to affect human health. What happens when you start feeding them evolutionarily novel nutrients? I'm not claiming that it has any measurable effect, good or bad, but from a precautionary principle viewpoint it seems to me a bad idea.

Carbohydrates used to come from fruits (with fiber), vegetables (in small amounts & with fiber), and starchy vegetables (starches are complex & slow to digest). Today, carbohydrates are consumed in simpler forms and refined to be more concentrated.

In the former case, they digest slowly. In the latter case, they digest quickly. The practical implications of this are immediately obvious if you have ever heard of glycemic index and glycemic load, but in short, fast digestion & large quantities results in a big spike in blood sugar which is hard on your body & leads to diabetes.

Also important is that the original forms of carbohydrates came with all kinds of other nutrients. A sweet potato includes vitamin A, vitamin C, manganese, copper, pantothenic acid, vitamin B6, potassium, niacin, vitamin B1, vitamin B2 and phosphorus. Sugar on the other hand is the quintessential "empty calorie", carrying no vitamins, minerals, only calories.

But clearly not frequently enough, hence the obesity...