Greetings!
I find the Pegaso to be the better equipped bike between the two. The fuel tank is much bigger, it comes in either carb, or fuel injection models, and it is better looking than the Beemer (and this is highly subjective mind you

).
I, myself own a Suzuki DR650, but had I not purchased an XR80 for my young son, the Pegaso would have been the Dual Purpose mount of choice (the two other bikes I had been considering were a Sportster

, and a Buell M2

).
Might I suggest that you check out
www.f650.com for further insight into BMW's thumper? These good folk have first hand experience with the bike, but there are a few that own the Aprilia, and they post there on occassion. There are still problems with the 2001 model F650's fuel injection. This is addressed regularly on the site's message board.
Either bike would doubtless serve you well. Good luck with your choice my friend!
The Toad