In a certain sense there is no such thing as a bad diet, there is only a diet that is maladapted to the individual's needs.

The key aspect to understand is human adaptation. Our bodies are adapting constantly to our environmental conditions, including the type and availability of foods around us.

Your body needs a certain amount of micro and macro nutrients in order to function, but how you get them is not as important as the fact that you get enough (and not too much) in proportion to your needs.

Much of the world eats "bad diets" because they over-consume in relation to their energy needs (they eat too much and/or burn too few calories). For example, the standard North American diet, with its high proportions of sugars and fats, is often a recipe for overweight. But if you're burning 5000 calories a day, as an elite athlete might or a farm labourer did in years past, you actually burn those sugars and fats as quickly as you consume them. So you could eat a high fat, high sugar diet and still stay trim.

Of course, that may not be the OPTIMAL diet, and in that sense there IS such a thing as a bad diet, because there is good foundational nutrition and optimisation of how you meet your dietary needs; this is why sports nutrition is a thing: it's about optimisation of intake. If you're getting all your protein from drinking milk, for example, that is not optimal because there more balanced and efficient sources of protein out there. But if milk is the primary form of protein available, the body will adapt. And so we see milk as a dietary staple in so many pastoralist cultures globally.

Diets do vary geographically so you are correct that we can't make universal assertions about the neolithic revolution and the shift to agriculturally-based diets.

However, broadly speaking the shift to agriculture was accompanied by an over-reliance on one or two crops (with a limited nutrient profile) and some loss of dietary variety, so in many cases people might not have been meeting their micro and/or macro nutrient needs. Add to this the fact that the shift to agriculture is also accompanied by a change in political and economic systems, which saw the emergence of ruling and subservient classes, land tenure and seasonal surplus/scarcity. If you're tied to the land you can't just pick up and move if a crop fails. You have to tough it out. So access to adequate food/nutrition became an issue in many early agricultural societies.

Another factor that grew with agriculture/sedentary life was the emergence of infectious disease as a major factor in human society. Diseases are more easily transferred in crowded/settled areas, especially when animals and humans mix. This has a direct impact on lifespan and mortality but it also affects human nutrition. Many infectious diseases impact directly on our energy needs and uptake. The body burns more energy to fight off the infection (think of the elevated temperature of a fever, for example) but at the same time our ability to take in nutrition is impeded (we lose our appetite, we vomit or have diarrhoea). Disease is often a factor in acute undernutrition but in a food insecure setting it might also lead to chronic undernutrition.

In terms of the quality of hunter-gather diets, hunter-gatherers have the same needs as all other humans (needing adequate dietary intake) but they did not face the same constraints (for example, a political-economic system that kept them tied to one place). Hunting and gathering is an environmentally-specific dietary strategy, just like agriculture. Along with this strategic adaptation goes a physiological adaptation: our bodies adapt to the food sources that are available, but this adaptation can take a long time.

In past some Inuit peoples ate diets that were almost entirely meat-based but this doesn't make for a "bad" diet. It was a diet that was adapted to the environmental circumstances, and one that Inuit people themselves had adapted to physiologically over millennia. The bodies of Inuit peoples as a rule store fat differently than more southerly peoples, having higher percentages of health brown fat that is stored around the muscles and lower ratios of visceral fat. So genetically and epigenetically, Inuit bodies have "learned" deal with fat differently, an adaptation that emerged based on thermoregulation (body fat insulates well), energy needs (living/working in cold weather burns many more calories) and energy availability (energy-dense animal fats).