Both are awesome.
One reason I prefer the 1D for sports and fast moving objects is not because of the FPS, but more because of the crop. The AF points fill up more of the viewfinder with a crop so it's easier to keep your subject within the ring of fire... especially when they're moving erratically.
I too wish the 1Ds had an ISO6400. I also find the 1Ds3 seems to handle servo focusing for very slow moving objects better than the 1D3. I was told because the the 1D3 AF is jumpier because it's optimized for 10FPS while the 1Ds3 is optimized for 5FPS. Dunno if that's true or not.
I believe only the 1Ds3 supports UDMA CF cards though.