Although not exhaustive, this article goes into some very sensible analysis of possible reasons why Rossi ( and many other riders ) struggled so badly on this bike.
http://www.motomatters.com/analysis/...mosedici_.html
I do not believe that Stoner is some super hero who could just jump back on that bike and win against the competition from Honda and Yamaha at the moment. There is very little to be compared between the spec of Ducati on the tyres he was using, against the Ducati of the previous two years on controlled tyres.
The only way to compare rider against rider is over a long period of time on a variety of machinery. Both riders are up there at the top of that leaderboard with little to separate them. But one thing is for sure, Rossi's results were impressive right up the end of the last Yamaha season he was with them, shocking for two years on the Ducati, and he now seems instantly back on the pace.
Ducati have been 2 seconds or more off the pace on works bikes with almost all their riders. That to me sounds like a pig of a bike.