Its gotta be the 998R - or even better the 996R!!!
Ducati have attempted to go to mass market appeal with the 999 and have by any reasoned, independant view, missed!
The 999 is built at a cheaper budget, using less parts than the 998 type and has been built to appease a fickle market place that is driven by a perceived need to want ride the latest and greatest technology every year.
Ducati had to evolve, economics and market pressures determined that - but if you want the latest and greatest superbike, you go look at the Japanese offerings (yep - I've done that).
But if you want emotion, soul and a reluctant envy from every other motorbike rider, get the archetypal 916.
The 996R is the best of this breed, but settle if you must for the 998R.
Tim