Both very valid factors. I was thinking a bit before your post that 12.7MP vs 8.2MP (within the Canon options at least, or within the price level of the 5D) is probably more important overall to the desirability of the 5D than the much talked about high ISO and high DR. And to be slightly cynical, Canon's possible holding back of EF-S format a bit to maintain unique selling points for 35mmFF. Will there be a 10-12MP high end EF-S model to replace the 30D once there is a higher resolution replacement of the 5D? (maybe 16.5MP, using "1DMkIII pixels").
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I think threads like this are useful in 'fleshing out' many of the factors that have a bearing on technical image quality, the pros and cons of particular formats with differing pixel densities and differing noise performance in relation to different camera/lens combinations, but the one unknown factor which tends to throw a spanner in the works, especially with regard to making the best personal economic decisions, is what's round the corner.
Many of us either cannot afford to buy (or cannot justify the purchase of) whatever system is currently on the market that best meets our requirements for the particular type of photography we may be interested in at a particular time, so we have to make some sort of assessment as to the significance of such pros and cons in relation to the general type of photography we think we'll be engaged in.
For example, right at the moment, a good combination of cameras for a wide range of (effective) focal lengths from wide angle to telephoto, would be the 12.8mp 5D and the 10mp 400D. But how would one feel if in 6 month's time Canon released a 22mp upgrade to the 5D with ISO 6400 capability and no more noise than the 5D currently has at ISO 3200?
That one 22mp camera could do everything the other 2 could do, and some. There would be no need to mess around changing cameras with the 100-400 IS zoom in order to get a longer effective reach and possibly lose the photographic moment in the process, and the extra ISO performance would allow use of f8 in circumstances where f5.6 would previously have been used.
And of course, needless to say, at shorter focal lengths 22mp is always going to be better than 12.8mp for large prints. The difference in pixel count is great enough to be noticeable. It's unlikely we'd have the same confusion that sometimes existed when the 5D resolution was compared to that of the 1Ds2. 16mp versus 12.8 is subtle. 22mp versus 12.8mp is not, I would think.