There is some white noise in players H/A spilts. As a whole, players have an OPS about 40 points higher at home. Upton's H/A splits for 2009 & 2010 fall with that norm, Last year he battled a thumb injury all season which could easily explain why we wasn't able to drive the ball (decrease in XBH%,HR% and HR/FB) so you end up with 2011 being the outlier.
Any player moving from a hitters park to pitchers park is cause for concern but I think in Upton's case people are only looking at the surface of what the stats tell us.
Just to add to your point, people were saying Matt Holliday couldn't hit outside of Coors Field before 2009.
