Upper requires a pulley-press to remove and install and you have to be careful not to damage the bearings. Also, since an upper pulley reduces surface area they are more prone to belt slippage.
With a lower pulley a boost increase actually reduces slippage. Plus, its easier to swap (15-20 minutes). You can also buy a "quick change lower". With those, you install a special bracket on the crank, and then special pulley's of different sizes (one for the track, one for the street, one for a road-trip/mileage, etc.) can be quick swapped on it in about 5 minutes.