I have followed Canon closely since I bought my 5D four years ago. I have seen the 5D claimed to be the best camera ever made, I bought the Mark II even with the "spots" and the claims that the D700 had much lower noise. Since that time I have learned much about cameras and imaging. I see two factors which Canon must surely be aware of:
1. AF has been an issue for Canon since before the 5D. The introduction of the D300 (which I owned) and it's AF which had all the same features as my old Canon EOS 3 film camera highlighted the deficiencies of the 5D and lower end AF systems. The 9 point system might be adequate to APS-C size sensors but it really doesn't work well for the larger sensor. The fiasco, real or imagined with the AF for the 1D IV has pushed the point home. Canon is clearly responding as demonstrated in the much better AF in the 7D.
In comparing to Nikon, many of the complains are debateable. Differnet processing techniques are mostly responsible for any percieved issues with noise. Nikons, except for the D3x are show uniformly less detail than even the old 12 megapixel 5D. These are choices each company has made in their approaches to making images. My observation is that on the whole the general opionion (not surprisingly) is that Nikons have less noise and Canons have more detail and that the differences in both are for the most part of minor concern.
Poor AF, on the otherhand is not a minor concern. In my opinon it is something Canon must address in all their higher end cameras. Their main user base is happy with the lens lineup, they are happy with the resoluition and the noise - they are almost uniformly not happy with the AF.
2. 5DII displacing the 1Ds. May pro's use the 5DII instead of the 1Ds. Since the image quality is almost identical and video is not all that important, the reasons are fairly obvious. The cost and weight differences over come the poorer build quality of the lower end camera compared to the 1D range.
These two points, AF and 5DII being preferred to the 1DsIII are the two largest issues Canon must first address. Nikon and Sony also give some indication of where the technology must go. Most of the other complaints, ergonomics, noise, AA filters, build tend to be periferal both to the the photographic market and to the making of photographs. I don't believe they are really the drivers.
My predition is the next FF camera will have:
AF system simlar or better than the 7D, perhaps it will be adjusted to the larger sensor size since upscaling the AF has not proven to be a good engineering solution.
Size similar to or slighly larger than the 5DII. Weather sealing and build comparable to, or similar to the 1D serices.
Megapixes similar to the pixel density in the 7D which is well proven. (Around 28M in FF). Smaller pixesl start to compromise dynamic range and push diffraction limits.
Pixel binning to achieve noise and processed noise levels similar to the best Nikon cameras.
In my view these are the issues Canon must address in order to maintain it's market lead in the pro market. The AF in the 7D and the number of new high resolution lenses such as the new 70-200, 100L macro suggest to me Canon is not about to lose that market because they can't or won't make a camera that addresses them.
A FF camera a bit larger than the 7D, with the same pixel density as the 7D, properly upscaled AF system similar to the 7D, slightly better processing to optimize high ISO photography and a little bit better build would have them lining up for years.