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Best was hurt by the fact that he was injured his junior year and left after three years of eligibility, so he was only the featured back for one full year. He'd be higher had he been healthy all of 2009. Likewise, Arrington was only the featured back in 2004. The site seems to emphasize production over multiple years, which is why Lynch gets ranked higher despite never having a monster season (though as the article notes, he was P10 Offensive POY). Like Stepfan Taylor, he gets credit for putting up stats consistently over multiple years (2 as a starter and one as Arrington's backup).
Or, put another way, only one player is ranked higher than Arrington despite having fewer rushing yards, and Maurice Jones-Drew had 1300 receiving yards in his career, and only MJD and Arrington are ranked higher than Best despite having fewer rushing yards. In fact, Arrington and Best have the fourth and fifth fewest yards on the list; only MJD, D'Anthony Thomas (another guy with big receiving and returning numbers), and Gaffney, who is the last guy on the list have fewer career yards. On the basis of career production, it is harder to argue that Arrington and Best deserve to be higher on the list.
Now, if you want to argue that Best (especially) is a better running back than a lot of the guys on the list, you can make that argument. That's what's fun about these sorts of lists.
BC