MiLB seems to be like a year behind on a lot of their rankings, every time they make a list. They also seem to favor the well known guys a little too much (by that i mean they favor guys that are well known among the general public, not prospects who have emerged in the last year or so, and they favor guys how have somewhat plateaued and may be busts).
For instance IMO (and really this is all about opinion)
Johnny Cueto should be much higher
Ellsbury is overrated
Andrew McCutchen, Homer Bailey, Adam Miller should all be moved down
There are a few other more minor things i disagree with, for instance i would rank Buchholz, Joba, and Kershaw in that order. not the reverse, but i can easily see how they would rank them the other way.
"I do not think baseball of today is any better than it was 30 years ago... I still think Radbourne is the greatest of the pitchers." John Sullivan 1914-Old athletes never change.