I played around a bit with the codec available at http://wildtramper.com/sw/cr2/cr2.html,
which allows you to specify whether you want to extract the embedded jpeg or the actual raw file. It looks like what I posted earlier was the embedded jpeg (thanks for pointing that out).
Color correction is not applied to the raw file by the extractor, so the colors are obviously off. The resulting size of the raw file was also about 5.8 MPix (1/4 the sensor resolution), so I assume that it does not do any sophisticated demosaicing. The jpeg was 22.1 MPix.
If someone has a 5d ii raw file with a similar composition, lighting, and iso, we should be able to get an apples-to-apples comparison here to see how the new sensor performs; just follow the same steps I did and post what you get. Obviously without the correct color profiles, the pictures will not look correct but, if the extractor does the same thing to files for both cameras, we can still make a comparison. Obviously there is the risk that the actual cr2 file format changed somehow between camera revisions, but I think its worth a shot.
I extracted both the jpeg and the raw file (as a tiff) using the program linked to above, then cropped using GIMP. I am going to try posting as a lossless .png first but, if I have problems with that, I will post as a jpeg saved at 100% quality.
Note: the image from the raw file is first, the embedded jpeg is second.