The Tuono will cost you a LOT less than the Duc in maintenance costs. I've only ridden a standard Monster 900, so I can't speak to the motor's performance, but I much prefer the chassis of the Tuono, I can tell that already. I've also put in excess of 20,000 miles on a Mille in a year and can speak to its impressive reliability. I never had to do anything besides change oil, filter, chain, sprockets, and tires.
Don't listen to the guy who says the Monster sounds better. The Tuono sounds glorious with any number of aftermarket pipes, which isn't to say that the Monster doesn't, of course.
As for looks, I think the Tuono is better looking, too. I've had several women (one is my fiancee, admittedly) tell me that it was the sexiest bike they had ever seen, but who cares what it looks like when you are on it, right?
I imagine that the Duc is more frequently stolen, just because there are so many on the road, the parts market must be there. Aprilia's did seem pretty safe from theft, although that didn't stop a couple of joyriders taking my Mille and totalling it earlier this month. I wanted a Tuono anyway, so I guess I can't really complain.
--sam