Why not ask the pro's? Doug Polen is a Ducati'holic. I think he puts this very nicely. What I got out of the article...
If you can ride like Bayliss, the 1098 should be faster (around a track...I think its obvious the 1098 has more power and is faster in a straight line). If you ride like most people, the 999 seems to play better.
http://www.fasterandfaster.net/2007/05/doug-polen-not-so-impressed-with-ducati.html