Agreed, I think there are issues with modern food that make folks more likely to be in poor shape.* But some diets strike me as going too far in reacting to that by appealing to nature.
With paleo, legumes are prohibited because of phytates, but spinach and chard, and are cooked lightly (if at all) compared to beans, aren't, despite their oxalic acid content.
IMO for people who are overweight by, say, 20 lbs or more, calorie reduction will have the largest impact. To the point where recommendations based on meal timing & micronutrients (or even macros, to a certain extent) are only useful in that they might help with compliance.
(Which might still make them very useful. Good compliance is 100% necessary for success. But what works for compliance varies from person to person.)
As one gets closer to the ideal weight range, some fine-tuning might be in order, but I think it's important not to let such things take priority over plain old energy balance.
* Without getting too deep into it, I think hyperpalatability is the big issue -- the practice of adding synthetic flavoring to foods has done a number on our collective palate, and made high-calorie, low-nutrient foods more appealing than they'd be otherwise. The same techniques used to used to fatten up livestock are used to drive food sales, with predictable results.
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