My only dealings with Aprillia was an MOT. Very poor service and useless parts availability- 6 weeks for brake pads

(I took the bike to another test station and it passed, so there was a con going on somewhere).
The F650 has two big issues, the water pump has no bearings and so destroys the seals allowing water and oil to mix. It's easy to spot, the oil goes light brown and easy to fix, with a forty quid kit from Motorworks/Motobinns and about 2 hours. If this hasn't been caught in time the heat warps the head and it's new engine time. I don't know if the BMW kit fits the Aprillia. The second issue I know about is the VR, they cook and you loose charge. Never got to experience that one first had. Most bikes will have salt damage, the paint is very very thin and flakes off (they all do that Sir

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Personally, I found the F650 a joy to ride but wouldn't touch one with a long pole now, the build quality is ****, neither BMW nor Aprillia were every really interested and the design was all look over function and too complex as a result. You don't need two carbs, five valves and watercooling to get 48 HP.
Andy