It's a V4, not a twin. The generally-accepted argument was that only Casey Stoner had the particular skills to ride the carbon-fiber monocoque chassis and supposedly brutal power delivery V4 to victory. It was big egg on Rossi's face that he couldn't win on it after they tried all types of modifications - even going back to a twin-spar aluminum frame - to make it work. You can look up a lot of articles on what MotoGP watchers speculate to be the problems - lateral/torsional stiffness, weight transfer, Bridgestone tires, etc.
The other thing was that Honda and Yamaha keep raising their game every year. So if Ducati goes in the "wrong" direction with development, they end up even further behind. The guy behind the current design, Felippo Preziosi, has already been moved out of the way and left the company. IMHO to keep tweaking a design in hopes of improvement when the guy who dreamed it up isn't even around is spitting into the wind. They need a dramatic change, more like a clean sheet design. You have to believe that is what the Audi brass is demanding behind the scenes now that it is their money being spent.
Rossi did score two podiums on the Ducati, both in the wet, which I believe showed he still had skills as rain is the great equalizer in racing. It was the dry performance of the bike, which in 2011 was still an 800cc, where it was clearly behind the others.
I know, I know, I'm a Rossi fanboy. It's only because he's the GOAT