We would all have to be very smart (smarter than any human) to know why these diseases exist.
Maybe it has something to do with the flesh being less important and the soul being more important?
Yes, the soul suffers the pain of the body. But when that connection is gone, so is the pain.
With all due respect, I find it quite interesting that I am asking these questions in the context of intelligent design as a scientific theory, while most of the responses have ignored intelligent design and gone straight to religion.