That is a fascinating and thoughtful article.
Moreover, it is
extremely funny if you think about all the baying for "fast, wide primes" for various digital systems (especially micro 4/3). Apparently, super-fast lenses not only aren't that much brighter, but in some cases they won't even buy you shallower DOF!
Now, that said, the "CCD advantage" in the M8/9 has almost nothing to do with CCD structure (as implied but NOT demonstrated with
data in the linked article). Rather, the advantage of the M8/9 comes from the use of an eccentric microlens array. In fact, the requirement for that specialized array is specifically
because the CCD sensor prefers to see light entering normal (perpendicular) to the sensor plane.
Note that an eccentric microlens array is also being used by Fuji on the APS-C,
CMOS sensor for the X-100 — which is fitted with a fast (f/2) wide angle lens.
Fuji knows what they're doing.
For BOTH CCD and CMOS sensors, the best approach will eventually be to use backside-illuminated sensors (back-illuminated CCDs have been common in scientific imaging for well over a decade, and back-illuminated CMOS sensors are increasingly prevalent in
consumer devices with small sensors). A good article that shows how beneficial backside illumination can be is
here (scroll down to Figure 3).
By putting the photosites closer to the sensor surface, the "tunnel effect" is minimised and quantum efficiency can be nearly perfect (approaching 100%).
Unfortunately, making large back-illuminated sensors is still
very expensive. Too expensive, at present, for 4/3, APS-C, and larger sensors. And these sensors, because they are very very thin, are (mechanically) fragile — and the bigger they get, the more fragile they are. Not rugged enough to put in a Nikon D4, yet. But maybe by the time the D5 is out...