I own both a 2006 KTM Superduke and a 2005 Ducati 749R with Leo Vince race pipe. Been riding for about 12 years, couple of track days under my belt - far from an expert but an ok rider. I am soooo much faster on the Superduke. The 749R is gob smackingly beautiful and the handling is fantastic. However, probably due to my age and creaky joints I cant fling it around fast enough to hang with Duke - benchmark is a buddy of mine on a K1200S who rides like a demon and he just cant get away from me in the twisty stuff when I'm on the KTM. If I was a better rider, I guess I would be able to get the 749 in exactly the right RPM range, but there you go.
Ducati is not that expensive to maintain, very reliable. KTM I feel is just bullet proof. Checked out the Tuono when I looked at the Superduke and never regretted my decision for a second. Hope this helps!
Cheers!