You have pointed out some of the reasons the Sony 16MP sensor is still the best APS-C sensor ever made!
Just looking at the D7000 sensor cross section, it's amazing how clear a path there is from the microlens into the photodiode because of those narrow wiring interconnects.
It got me thinking... on a per pixel basis, the D5200 doesn't give much to the D7000, not as much as you would expect. Ordinarily, as you increase the megapixels and the photodiodes get smaller, the wiring takes up a proportionally larger area. Which brings us back to the idea of the Toshiba copper fab. I wonder if they took advantage of the higher conductivity (over aluminum) by again reducing the size of the wiring interconnects. That would claw back some of the light gathering ability lost in shrinking the photodiode.-- hide signature --
Of course they did. But also deep submicron fabs have switched to copper anyway for other reasons, such as current handling, R*C delay, and patterning ability.