Take a look at this review page of the 5D mark II:
Canon EOS 5D Mark II Review: 3. What's New: Digital Photography Review
They state, that the gaps became smaller compared to the original 5D. Also they mention, that the 50D has a gap-less design. So the gap-sizes seem indeed to vary across different camera models. But if all kinds of sensors have a QE of 55% at a certain wavelength, I interpret this as an indication that often the same semiconductor material is used and the QE is just a property of this material and not the whole sensor with all its microlenses and complex engineering-stuff. But I may be wrong.
How did you measure that?
1 GPixel/s would be enough to read 22MP 30 times per second. So do you think that it is possible but too expensive, to build it into a $3000 camera within the next years?

Yes, and that is one reason why smaller pixels tend to perform better than larger pixels if you don't control for technology level (as I'm sure you already know).

The original 5D had a QE of 25%, the 5D2 improved this to 33%. The move to gapless microlenses in the 50D improved QE from 33% in the 40D to 38% in the 50D.

Take several raw files of a colorchecker chart, plot the values of the gray patches, and the slope gives the inverse gain (ADU per electron). From there all that's needed to calculate the QE is the ISO calibration of the camera (one camera's "ISO 200" may be another camera's "ISO 500"), but figuring that out requires some sort of calibrated lighting system and highly accurate light meter. So I just use measured ISO numbers from DxOMark.

Yes, that's my guess.

Couldn't you just use larger pixels while in video mode? It seems like a straightforward way to optimize it. If you increased the pixel size so that the data was being read as a 2 or 4 megapixel video image it seems like it would a. increase light sensitivity and b. severely reduce the aliasing common with high pixel images.

Or did I just get off at the wrong train station?

How do you increase the pixel-size without physically replacing the whole sensor?

My understanding is that you don't literally have to read every point of data on the sensor as a pixel. You can choose instead to use an area with several physical points of sensor data as a single pixel. For example, you could read every 10x10 points on the sensor as 1 pixel for your image. Generally the bigger the pixel the better low light performance. Additionally, lowering the image size to 2-4 megapixels can also significantly lower aliasing artifacts.

Well it sounds like a win-win anyway, but camera manufacturers have been shy to go down this route, so there may be a good reason it hasn't been implemented. But it still sounds logical to me, or am I nuts?

So you want to read out the average value of multiple pixels with just one read-out operation? I don't think that's possible, without designing a whole new sensor. But I think it sounds like an interesting idea.

I thought this was being done in most cameras and camcorders anyway. There's a single read operation from the sensor and then compression is applied to raw sensor data to give us the final image. The larger pixel idea would be applied after the raw sensor data was read.

That's pretty much what I was talking about. The rumour (again, I don't want to perpetuate or confirm it) is that Canon is working on sensor that does just that in video mode. I don't know anything about any future cameras but the logic behind the rumour seems to make sense.

Although a 10x10 pixel area might be a bit large. That would mean that to get a 1920x1080 image, you'd be working with roughly a 220mp sensor!

There's a read-out operation for each individual pixel, not just for the one frame! That's why 5DmIIs video has a lot of aliasing, because only every third row and column gets read out to reduce the number of read-out operations per frame. If you want to make a virtual larger pixel, you would have to read out each native one within it first. So you wouldn't cope with the problem that the number of pixels which can get read out per second is limited. Btw. calculating the average out of a block of pixels and building a new frame with smaller dimensions out of these blocks is equivalent to apply a box-low-pass-filter and then downsampling to the raw data.
I initially understood your idea, that the sensor gets designed in a way, that multiple pixels can become connected to additional operational amplifier circuits, which generate the average values in an analog way, and only the output of these additional circuits gets read out.