It seems to me like prospect rankings should simply reflect who the author would rather have in his or her minor league system (assuming a generic system).
If someone was given the choice between Graterol and Gordon, and would rather have the former, then it makes sense for Graterol to be ranked higher regardless of "likelihood."
The BA top 10 only stands out to me with respect to Kirilloff and Jay. The former doesn't project to bring a ton of defensive value and hasn't had the chance to really show anything yet. Jay is a reliever with some recent injury issues.
While the low ranking for Gordon is an outlier, it's not necessarily crazy - if Gordon wasn't a first round pick with his family history, he almost certainly would be getting less attention. An OK-fielding second baseman who can't hit lefties has basically no value.
I think he certainly can be more than that, but he has plenty of AAAA risk, which is just as significant as the other risks prospects can have (e.g., injury risk, lack of exposure to advanced competition, etc.).