I rode the Aprilia Factory and The BMW S1000RR back-to-back for 1/2 an hour each down some really fun local roads, thinking I was buying the Aprilia.. Instead, I bought the BMW.
The Aprilia is brilliant, just brilliant.. Handles like my 675 Daytona and feels about the same size.. takes the turns better than any other Liter Bike I have ridden and makes the most amazing noises.. like aural sex..
The downsides to the Aprilia are the lack of power compared to the BMW, the amount of heat that comes up to the rider from the engine and the fact that it feels heavy.
The BMW is so close to the Aprilia in handling, has appreciably more power and far better brakes. The BMW has a more comfortable riding position for me and given the price differential, the BMW made more sense for me.. However, I might still buy the Aprilia and keep it as my Weekend toy.. The BMW is my everyday commute Bike, as well as Weekend turn carver.
In short, I think that the BMW and the Aprilia are the two best Liter class SportBikes out there and you just can't go wrong with either one..