Just a few thoughts. When a new Canon model comes out, I usually check the dpreview noise and resolution charts, after they get around to publishing their in-depth review. It seems to be the case so far that Canon never introduces a new model that has higher pixel noise than a previous model. On the noise front, it seems Canon refuses to go backwards (with regards to DSLRs anyway).
Many people were disappointed the 30D had no more pixels than the 20D. I guess it's because Canon were simply unable at that stage to provide smaller pixels that would not also be noisier. But I'm confident they are working on it and that we'll see more pixels on the next generation of cropped format and full frame sensors and those individual pixels will be no noisier (and possibly even less noisy at high ISOs) than the current 30D and 1Ds2 pixels.
Another issue is the effect of noise on a given size print. Most of us do not restrict ourselves to making prints of a size that does not require either upsampling or downsampling of the image file. If we did, we'd be restricting ourselves to a 12x18" print for the 5D and a 9.5x14' print for the 30D. When we upsample (interpolate) an image to make a large print, we interpolate the noise also. The reverse is also true.
The consequence of this is, for any equal size prints, big or small, the sensor with the greater number of pixels will produce less visible noise, provided the smaller, more numerous pixels have, individually, at least equal noise to the larger, less numerous pixels on the other sensor.
I'm also of course confusing pixel size with pixel pitch, which I think is forgivable because Canon never seems to make public the actual pixel (photodiode) size. But, as DiaAzul mentions, there's probably scope for improvement here by reducing the space on the sensor taken up with on-chip processing, whilst keeping the actual size of the photodiode the same, even though the pixel pitch has increased. However, it's not clear to me to what extent there might be benefit here. As I understand it, the microlens directs the incoming light onto the photodiode, whatever its size, so the photons are not wasted by falling unproductively on processing transistors. Nevertheless, a physically larger photodiode should translate to a greater full-well capacity and greater dynamic range. It's worth noting that, according to some facts in a Canon brochure on the D30 (not 30D), that Michael referred to in a thread a few years ago, the actual pixel size of the 10 micron-pixel-pitch D30 is only 5.25 microns. (I know! I've got a good memory, for some things ).