Arash,
I recently returned from Tanzania where I took my 1D Mark II and 5D Mark II. I initially was using the 1DII on my 500 f/4 and 5DII on shorter lenses for scenics and large close animals. Occasionally I would switch the two cameras. The 5DII has pixel pitch the same as a 20D and 30D, so one still has the "reach" of those cameras if one wants to crop. After about 3 days into the trip and reviewing my images, I found I had much sharper images and a slightly higher keeper ratio (meaning extremely sharp focus) with the 5DII. For me this ratio is around 90%, but degrades as the speed of the subject increases. As the speed increases I experienced the 1DII gets close but not quite good enough focus. The 5DII either nailed it with an astoundingly sharp image or completely lost it. But for the subjects I was shooting, the 5DII was the clear winner for me. So after 3 days I shot mostly with the 5DII, only going through about three 4-GB cards on the 1DII for the rest of the trip. I did have to resort to anticipating the action more and rely less on high frame rate. This did result in failure to capture several small birds in flight at takeoff. But the advantage of the large sensor is that I knew I could crop to 8 megapixels to get to 20D/30D class images and have the space for those shots when the wings are fully open and not have to worry about fitting in the frame. So the 1DII for will be for the really small fast birds and the 5DII for everything else. (Now hoping for a 1D Mark IV with 20+ megapixels at 10 frames/sec.) :)
I should add the for moving subjects I use Av, AI servo, and a single focus point. I move the focus point around to keep a focus point on the eye of the subject and giving the composition I want. That way I do not have to set focus and reframe at any time.
I only have a few images up from the trip, at (some have commented about how cool it is when you can say things like "cropped to 14 megapixels"):
http://www.clarkvision.com/galleries...009/index.html