I found the best stats for QB ability seem to be yards/attempts, and attempts/TD. To me these seem to capture how successful the QB is at delivering the ball to the best target and scoring ability.
I took the sagarin schedule score and used them to normalize the results to account for opponent difficulty.
Based on this, the best QB's post DP (excluding 2000-2002) using yards per attempt are:
Year---Conference---Coach-----Quarterback
2009 CUSA Jones Padron
1996 WAC Rossley Flanigan
2006 CUSA Bennett Willis
2011 CUSA Jones McDermott
2010 CUSA Jones Padron
2004 WAC Bennett Eckert
1993 SWC Rossley Flanigan
1992 SWC Rossley Freiburger
2007 CUSA Bennett Willis
2008 CUSA Jones Mitchell
1999 WAC Cavan McCown
1994 SWC Rossley Flanigan
1990 SWC Gregg Romo
2005 CUSA Bennett Romo
1989 SWC Gregg Romo
1995 SWC Rossley Canine
1998 WAC Cavan Sanders
2012 CUSA Jones Gilbert
1991 SWC Rossley Ritz
1997 WAC Cavan Sanders
2003 WAC Bennett Bartel
Now based instead on
Year---Conference---Coach-----Quarterback
2006 CUSA Bennett Willis
2010 CUSA Jones Padron
2007 CUSA Bennett Willis
2008 CUSA Jones Mitchell
1996 WAC Rossley Flanigan
2009 CUSA Jones Padron
1999 WAC Cavan McCown
1990 SWC Gregg Romo
1997 WAC Cavan Sanders
1993 SWC Rossley Flanigan
1992 SWC Rossley Freiburger
2011 CUSA Jones McDermott
1995 SWC Rossley Canine
1998 WAC Cavan Sanders
2005 CUSA Bennett Romo
2004 WAC Bennett Eckert
1989 SWC Gregg Romo
2012 CUSA Jones Gilbert
2003 WAC Bennett Bartel
1991 SWC Rossley Ritz
1994 SWC Rossley Flanigan
(Note this upload shows yards/attempt/sagarinratio. Should be yards/attempt*sagarin ratio. The rankings above reflect this change.
