The first subsection is "variation over time". The drop between the paleolithic and neolithic coincides with the development of agriculture.
This is a pretty contentious issue. The idea that humanity's single most (evolutionarily) successful technology caused a massive decline in individual quality of life is pretty disturbing, and some of the evidence is contradictory. It seems like a debate best left to experts, but I thought it was worth mentioning.
I still agree with the original post -- we're very lucky to be alive now.
I was actually going to point to Jared Diamond as well! In his book The Third Chimpanzeem Jared writes about the immediate decline of health that followed the introduction of agriculture. By measuring the health of teeth, and etc we can see a noticeable drop in the years immediately following agriculture.
Looks like the article you linked to covers the same material.
"We know roughly when and where farming began, because of the archæological evidence: domestication is a shock to the physiology of man and beast. The skeletons of people change, they temporarily grow smaller and less healthy, as the human body adapts to a protein-poorer diet and a more arduous lifestyle. Likewise, newly domesticated animals get scrawnier at first."
I'm sure some google wizardry could find a real source.
Read "Guns, Germs and Steel" and "The Third Chimpanzee" by Jared Diamond. He talks a lot about the rise of agriculture.
When we look at how the average lifespan is increasing, we're only looking at the lifespan since the start of civilization as we know it - allowed by agriculture. It's possible that our quality of life is only now catching up to what our hunter-gathered ancestors had.
Or are you using some other metric to measure what you call "healthier"?