As most anyone that follows the Blue Jays knows, Jose Bautista has a rocket arm in RF, but how much of an asset is his arm really. Using BIS (Baseball Info Solutions) data, we see that Jose Bautista had the extra base attempted 61% of the time, ranking 20th among Right Fielders in 2011 with at least 150 outs made. While he posted the 2nd highest kill % among Right Fielders, at 17%, opponents advanced on 50.5% of opportunities ranking 14th out of 24 qualifying Right Fielders.
In itself, the high Kill% and advance rates aren't awful, ranking 2nd and 14th respectively, but Jose Bautista's ranks on shallow (12th), medium (16th) and deep (24th) aren't very good. His rating (-8) on basic balls in play ranked 23rd out of all Right Fielders. Looking at the RF's whose arms didn't limit runners as much as Bautista, all were at least 4 runs better on basic balls in play then Bautista and were (minus Cruz and Ichiro) among the best at getting to deep balls, which can affect an advance % due to being better balls to run on.
In conclusion, the evidence shows that Jose Bautista isn't really an asset in RF defensively, and a defensive move to 1B or DH should be in the cards soon.