Stoner has never been known for his development skills. He was fast on the Ducati because he’d just got off the crap Honda’s they’d been giving him. He rode the Duke successfully for a year and, to be fair, he demonstrated that he’s the fastest man out there when he’s fully confident in what’s underneath him.
When he couldn’t offer sufficient, detailed feedback to make the Ducati work against the well-developed M1, he jumped ship for the not-quite-as-good factory Honda and repeated the exercise of winning on a bike that was “half right”. He’s still the fastest but, once again, it seems that he’s run out of ideas as far as improving the bike is concerned, and he’s been out-performed by Lorenzo and the M1.
As far as Lorenzo’s concerned, I’d say there’s an element of luck involved, as he doesn’t seem to have suffered the same tyre-related woes as Rossi, Stoner, Hayden and Spies, but; although Stoner seems to be able to ride around a problem, I’m not convinced that he can do what he’s paid to do – which is to help his engineers to solve the problem - so it becomes worse – to the point where he can’t ride around it – and then he has no solution and nowhere to go.
Rossi and Hayden now have a bike that is fast for one qualifying lap in the dry and which is very competitive in the wet: when they find a consistent race setup that allows them both to ride to their individual strengths in all weathers, the Ducati will be capable of achieving podiums - and even a top step or two - so it’s not been two wasted years. Even though they’ve not been productive in a dramatic way, they have made some progress, although it's impossible to pinpoint exactly where and how because the bike itself responds so inconsistently to setup changes.
Ducati will try to hang on to Rossi because that means they get the experience and expertise of his team as well. Whether Rossi will stick to Ducati is another matter.