When you're comparing cross generation, in most cases, it's really difficult to factor defense into the comparison. In terms of guys who have played the position their entire career, Honus Wagner, pretty clearly, is the greatest shortstop of all time. After that, I would say it's Derek Jeter, Arky Vaughn, Joe Cronin, and Ernie Banks in no particular order.
EDIT: As for your edit, that's a bit misleading, as he was close to average in 2008 and quite good in 2009.