I've done about 20,000 kms around the Middle East on a '97 Peg with no troubles whatsoever. I scooted around for days off-road around Rum Wadi in Jordan, did rock deserts in Iran, and did some mountain off-roading in Turkey. All this with about 150kg on the bike.
The bike is virtually identical to the F650 of the same year (most parts are interchangeable) and is fairly simple to maintain. If anything, the Aprilia has more attractive styling and (not surprisingly, being Italian) is a better looker.
The main criticisms of the bike are: some chronic faults such as head gasket (a fault it shares with the F650); appalling after-sales service (BMW to the rescue on engine and running gear but fairing parts are hard to get); slightly over-engineered in areas (especially electrical); a a dearth of them on the road (although a keen following means several good website forums).
The difference in cost between the Peg and the F650 has always been a mystery to me as they (apart from some styling) are (were) essentially the same (and I've ridden both extensively, including a '97, 2000 and 2003 Peg, and a '98 and 2002 BMW).
They are thirsty and, like F650s, need to be kept in tune to keep the petrol costs down. They ride well on- and off-road and are extremely comfortable over long distances with a great riding position .
My personal opinion: if you were presented with a Peg and an F650 in similar condition for similar price you should select the Peg for its looks or the BMW for the security of its popularity and abundance. If the Peg is much cheaper it really is a no-brainer.
All this goes out the window with the newest models as I haven't ridden them.
hope that helps.