i have an 07 550 with the original, zero mile engine in it with about 3300mi on it now. not one issue. insanely fun bike but can be expensive to maintain. frequent oil changes and early maintenance depending on how you ride it. same as any MX bike really, just double the parts.
back roads and track = hell yes. any slab at all = hell no. dropping a few teeth off the rear sprocket will help with droning through towns but the bike really is not meant for 'cruising' of any type.
the big issues to watch out for on the '06 - '07 models are proper setup (derestriction, mapping, tech bulletin updates) and case sealant problems that cause water to mix with oil. setup was probably the biggest thing to plague the early bikes. if you dont derestrict them correctly, apply all tech updates, then map to suit... you get burnt up starter motors and starting issues. if you dont change the oil correctly you get blow-by into the airbox (way common issue) filling the drain line. EDIT: a few other important setup points on the older bikes to check, black plastic oil filter cap was upgraded to an aluminum one, check, loctite and retorque the flywheel bolts, upgraded starter gears and upgraded mapping with 6 sec starter delay. Aprilia had dealers pressure test the motors, if they failed, they got an '08, black sealant motor.
the '08s seem to experience head gasket problems more than the older models but the case sealant issue was cured (for the most part). setup is still really important or you get some of the issues mentioned above. most dealers just don't know much about the bikes. for local shops, Seacoast and Wagner seem to know their stuff.
i may put mine up for sale, thinking about grabbing another dirt bike and ditching pavement altogether but i cant decide because i
LOVE the bike
here's a pic