Most 5D2 owners would have payed extra to get it better weatherprotected and with better AF. Canon should not have needed much money extra to cover these issues, while still leaving lots of differences up to a more expensive 1Ds body.
What might seem like a small difference can make a big difference in cost, particularly when it involves tighter manufacturing tolerances, metal machining, and hand fitting. The true weathersealing of the 1-Series, additional machined and fitted parts like the memory card door, and the tighter tolerances of the focusing screen and box are examples.

