14% seems quite a large shift.
Separately, even if we assume that protein yield per acre is increasing, if calorie yield increases faster then eating the same foods processed in the same way make us gain weight when it previously didn’t. If total calories per unit of protein goes up 1%, 2500 kcal per day with the correct level of protein becomes 2525 kcal per day, which isn’t much on its own but it’s every day for your entire life and adds something like 18 kg/decade to your body weight. 
(This does make me wonder how we were supposed to self regulate body weight in the wild).
 assuming a 100g/500kcal bar of chocolate is a representative model of human fat cells.
Finding food is uncertain, hard work.
That’s why my calculations was based on a number smaller than the lower bound.
> If you want more protein in your diet, eat more soybeans, meat, eggs, milk, or even protein powder of any form.
Irrelevant. Most people don’t eat what’s healthy (evidenced by the obesity epidemic), so people continuing to eat what they always used to eat resulting in them now being fatter than they expect is a problem regardless of the fact that “better” foods exist.
From the study: The largest was a 9.3 percent drop in the zinc level in wheat. They also found reduced levels of protein in wheat, rice, and peas, but not in soybeans.
Ok. A 9.3% drop in zinc on a per unit basis. First of all, not an alarming figure at all. Second of all, wheat is not a great source for zinc. It has phytic acid that prevents the absorption of zinc and iron .
Also says reduced levels of protein in wheat rice and peas, all single digit drops (again on a per unit basis more than made up for by increased yields under higher CO2). And again, these are not significant sources of protein. Soybeans are, and it clearly states that soybeans are not affected.
Plants evolved under CO2 conditions in the thousands of PPM. The carbon we're releasing into the atmosphere is ancient plant material. If you think CO2 has an adverse affect on nutrition, then you've got to explain to me how the dinosaurs got so big.
That’s terrible argument. There are plenty of creatures much larger than us whose diets we cannot survive on.
But for what it's worth, birds are the closest living relatives to dinosaurs and we have no trouble digesting birds for nutrition. In fact, chickens are the closest living relatives to Tyrannosaurus Rex. So we would have no trouble at all roasting a T-Rex and consuming it for nutrition were we able to hunt one.
Size: “thriving” is incredibly vague. Would you say plant life is “thriving” in the environment of the Blue Whale?
Abundant: how abundant? I have seen no estimates for primary production in the Cretaceous, as googling gave me paywalls.
Third point: Even plant species evolve to fit their environment, so for a discussion about plants that exist today (and, worse, which humans selectively bred to be full of calories) it doesn’t matter how much other life there was c. 100 MYA because the plants around now didn’t evolve for what was around 100 MYA.
Fourth point: depending on which era of dinosaurs you’re referring to, plate tectonics radically shifted global geology since then, changing how much coast there was, how much land was desert, where mountains were, and global ocean currents, so even if the plants and animals were the same as now, the total living biomass would be different.
Fifth point: the plants can still “thrive” even if they’re no longer what we consider “nutritious”. They can also still thrive even if something else does. Grass/cattle comes to mind, although the reasons are almost the exact opposite to this scenario.
I.e. that with adapting formulas of fertilisers no shift might be observed at all.
Plus if you read the what's linked it's a minor author correction on the 2014 article.
The original article was not linked but an author correction.
The author correction seems to only add some missing references.