There have been many, many years where the Cowboys front office made decisions that have come back to bite the franchise in the backside. Joey Galloway comes to mind here. From 1994 until the time Bill Parcells arrived, it seemed like nearly every decision blew up in the Cowboys face.
Yes, the drafting in the Parcells era was better than the previous eight seasons. Obviously, there were some real clunkers as Bill selected from his loyalty to his former players and his home area in northern New Jersey. I am speaking of primarily Carpenter, Fasano, and Miles Austin. However, it is the influence Parcells had on the front office and especially the scouting department in what specifically to look for in players that is paying off for the Cowboys today (I believe).
Since Parcells arrived, there has only been one horrendous draft (2009) and one highly questionable draft (2004). This all points to my belief that Stephen Jones heeded many of Parcells' words while he was here. Stephen, his father, and some of the scouts are the ones who have been around since 2003 (not counting players). The Cowboys have had only two losing seasons since Parcells arrived. When you throw in the transitions, losing salary cap dollars, and a plethora of injuries, that tells me that there is stability and good decision making in the front office.
I hate to say this, but the Patriots have benefitted from Parcells also. The Jets, on the other hand, are finally trying to clean up their own mess after a decade and a half.
Regardless, the Cowboys are going in the right direction.