You might be missing that maximizing heat collection while the sun is shining is not the goal, that too hot in the day can be just as bad as too cold at night, that each layer of "clear" polycarbonate (ie, 2 for twinwall) blocks about 10% of the light, and that gaping curtainless windows are not always a desirable architectural feature.

How many buildings have you been in that have expansive south facing windows? How many of them have been comfortable day-and-night year-round in a harsh climate without mechanical heating and cooling? Very few buildings achieve this, and I'd guess that none of them have large windows.

The Introduction to to the article is a good "introduction" to the issues. The rest of the article explains the introduction. If you are interested in the issues, it's a good article, worth reading in depth. But as the author says in the preface, "I’d suggest reading this when you’re in a “learn” mode – because if you’re in “skim” mode, you’ll just be wasting your time."

Shades can help with privacy, but what if you want the privacy at the same time you want to be capturing heat? And if requires active control --- well, that's by definition not passive. Interestingly, the new movement in high efficiency houses is frequently for low solar gain windows: well insulated windows with special coatings to admit less heat while still admitting light.

From another standpoint, gigantic expanses of windows are rarely the best way to build a pleasant room. As well as being a rare crossover between Computer Science and Building Architecture, Christopher Alexander's "A Pattern Language" has lots to say on this. Some excerpts here: http://kk.org/cooltools/a-pattern-language/

Which is to say that opaque heat-gathering walls serve a purpose that is separate than that served by windows. Both have their place, and they don't tend to replace each other directly.

The black box surface and vanes maximize the conversion of light into heat. The construction with the airflow traps and chimney effect maximize the transfer of the heat into the building while minimizing the heat transfer out of the building when the sun isn't shining.

Windows are not nearly as efficient because the material behind the windows is not optimized to convert light into heat (see his section on the design of the black vanes) and the airflow spreading the heat throughout the building will be poor compared to the design in the article.

The black vanes are cooled, during the day, by induced air flow, such heated airflow going into the building (passively), and results in heating the building, without further action. The panels are designed to prevent winter-night cooling via the panels. Thus you're missing the passive intent heating intent of the design: windows fail as a passive heat source, because of the need to actively insulate them in some fashion in the winter night.