Not to be glib, but [citation needed]. At least in the US, the food advice handed out by the USDA is generally considered to be accurate to the current information available to scientists. Everything I've personally seen contradicting it has been merely bare assertions without citation or data, or else points to a study done by a clearly biased group or individual. If you've got something substantive, I'd love to see it, as this is a special interest of mine.
Nope, the USDA recommendations are subject to an intense amount of lobbying by the large food companies. Anyone who thinks that government scientists are free to speak their minds hasn't worked in government, and unfortunately their scientific research is largely ignored or reshaped by economic and political forces when it comes time to make policy recommendations (see Reagan, R., under whose administration ketchup was famously considered a vegetable in school lunches).
If you really want to eat healthy, and wanted to eat what the science tells you is best, you might start with the research by Dr T. Colin Campbell and Dr Caldwell B. Esselstyn Jr. who did large-scale studies of the effects of eating processed crap vs. whole foods. See for example their books The China Study and PlanEat for citations, if you want to understand the evidence and know what to eat.
For the history of this, I recommend the anthropologist Sid Mintz who wrote Sweetness and Power, a history of sugar. In it he traces the shift in the British diet from healthy, farm-based foods to sugar-based foods and shows how that shift in diet was inextricable from the growth of cities and factories during the Industrial Revolution. In other words, he shows how the political economy of sugar has led to our present sugar and carb based diet. Unlike Campbell and Esselstyn, Mintz won't tell you what to eat, but he will tell you why everyone wants to sell you processed crap masquerading as food.
The upshot, however, is simple. Eat no-to-little processed, sugar, dairy and high-carb foods; eat only a little meat and some fish; eat a lot of protein-rich legumes, nuts, vegetables and whole grains. Drink mostly water; avoid sugary soft drinks, fruit cocktails and even too much juice. And cook for yourself; restaurants suck (from a healthy eating perspective).