I did some research on Baseball Reference measuring the offensive output of the Padres versus that of their opponents since Petco opened. What I found is that the Padres have been consistently out scored, out homered, and out slugged in every season except 2007, and in 2010 they out scored and out slugged their opponents yet were out homered.
Below is the chart form of the data that I found. Draw from it whatever conclusions you want, but it seems to me that the better team, e.g. the 2007 Padres, will consistently outhit their opponent at Petco regardless of where the fences are. I tried to make charts but the stupid SB Nation editor won't let me post them or upload them so go figure. Anyway, discuss: