I started with a Minolta X-700. It had no autofocus; AF lenses made their debut with the Minolta Maxxum a few years later and I subsequently upgraded to the Maxxum 7. The Canon 5D has a much more advanced version of AF than the old Maxxum. It may not be up to the standards of the 1D or Nikon CAM-1xxx, but it's actually more than I need.
For landscapes, cityscapes, and family/friends, it works quite well.
Regarding 3.9 fps, for me that is more than adequately compensated for by 30fps HD video at full 1920x1080. Whenever I need to capture action, I'll just switch to video and pick individual frames out of the video sequence.
The AF and FPS trade-offs in this camera simply position it for a different audience. If you are someone who depends on AF and FPS, all you need to do is realize the obvious: This camera is not for you.
Don't drop it in the sewer accompanied by endless rants of selfish disappointment coming from a realization that the camera isn't meant for you. Instead, just shop elsewhere. Pricewise, the 1D MkIII is the logical choice. It has enough megapixels and enough speed.
I am as impressed by the 5D MkII today as I was the day it was unveiled. It's still on my short list of goodies to buy. Not going to preorder though; I need to see more samples to judge image quality.